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Sample records for 7-fold bac library

  1. End Sequencing and Finger Printing of Human & Mouse BAC Libraries

    SciTech Connect

    Fraser, C

    2005-09-27

    This project provided for continued end sequencing of existing and new BAC libraries constructed to support human sequencing as well as to initiate BAC end sequencing from the mouse BAC libraries constructed to support mouse sequencing. The clones, the sequences, and the fingerprints are now an available resource for the community at large. Research and development of new metaodologies for BAC end sequencing have reduced costs and increase throughput.

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

    PubMed

    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. PMID:27511172

  3. Development of BAC libraries and integrated physical mapping of human chromosome 22 using BACs. Annual report, July 1994--June 1995

    SciTech Connect

    Kim, U.J.; Shizuya, Hiroaki; Simon, M.I.

    1995-12-31

    BACs and fosmids are stable, nonchimeric, and highly representative cloning systems. BACs maintain large-fragment genomic inserts (100 to 300 kb) that are easily prepared for most types of experiments, including DNA sequencing. The authors have improved the methods for generating BACs and developed extensive BAC libraries. They have constructed human BAC libraries with more than 175,000 clones from male fibroblast and sperm, and a mouse BAC library with more than 200,000 clones. The authors are currently expanding human library with the aim of achieving total 50X coverage human genomic library using sperm samples from anonymous donors.

  4. CHARACTERIZATION AND PHYSICAL MAPPING OF MAIZE BAC LIBRARIES USING HIGH DENSITY BAC FILTER HYBRIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A HindIII and an EcoRI maize BAC library have been constructed from maize inbred line B73. Use of both libraries to make a physical map should minimize the under representation of certain genomic regions caused by the use of a particular restriction enzyme. High-density filter sets from the two libr...

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

    SciTech Connect

    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.

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

    PubMed

    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. PMID:24243195

  7. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A 17.3-fold redundant bacterial artificial chromosome (BAC) library has been synthesized for carrot, the most-economically important member of the family Apiaceae. The library consists of 92,160 clones with an average insert size of 121 kb and ~ 2 % organellar DNA content. To provide an overview of ...

  8. Construction and characterization of a deep-coverage carrot (Daucus carota L.) BAC library

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The first carrot (Daucus carota L.) BAC library was constructed using imbred line B8503, which is nematode-resistant and accumulates carotenes in its roots. The BAC library consists of 92,160 clones comprising 22.4 haploid genome equivalents based on a genome size of 473 Mb/1C. Upon the analysis of ...

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

    PubMed

    Eggen, A; Gautier, M; Billaut, A; Petit, E; Hayes, H; Laurent, P; Urban, C; Pfister-Genskow, M; Eilertsen, K; Bishop, M D

    2001-01-01

    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. PMID:11712974

  10. Selection of chromosome 22-specific clones from human genomic BAC library using a chromosome-specific cosmid library pool

    SciTech Connect

    Kim, U.J.; Shizuya, H.; Birren, B.

    1994-07-15

    A new approach to rapidly identify chromosome-specific subsets of clones from a total human genomic library is described. The authors report here the results of screening a human bacterial artificial chromosome (BAC) library using the total pool of clones from a chromosome 22-specific cosmid library as a composite probe. The human BAC library was gridded on filters at high density and hybridized with DNA from the pooled chromosome 22-specific Lawrist library under suppressive conditions. In a single hybridization, they picked 280 candidates from the BAC library representing over 30,000 clones (or 1.2 x coverage of human genome). This subset contained more than 60% of the chromosome 22-specific BAC clones that were previously found to be present in the original BAC library. In principle, this approach can be applied to select a subset of clones from other global libraries with relatively large inserts using a pool from a regional library as a composite probe. It is important to note that the target and probe libraries must be based on vectors that share no homology with each other. 8 refs., 2 figs., 2 tabs.

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

    PubMed

    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. PMID:26438131

  12. Construction and characterization of human and mouse BAC libraries from sheared DNA

    SciTech Connect

    Shizuya, Hiroaki

    2002-08-23

    We have developed a new way to construct BAC libraries with small inserts using sheared DNA sources. Because of our use of the randomly sheared DNA as DNA sources, some regions of genome may be represented better in our libraries compared to the currently available and more conventional libraries constructed by enzymatic partial digestion. B263 We have developed a new fingerprinting method useful for physical mapping by large insert clones, in particular by BACs. It is based on four-color fluorescent labeling of fragments generated by combination of a type II and a type IIS restriction enzyme.

  13. BACTERIAL ARTIFICIAL CHROMOSOME(BAC)LIBRARIES CONSTRUCTED FROM THE GENETIC STANDARD OF UPLAND COTTON

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two BAC libraries and one plant transformation-competent BIBAC library were developed from the Gossypium hirsutum acc. TM-1 for the development of an integrative cotton physical and genetic map and other genomic applications. TM-1 is the most desirable choice for the physical map of Upland cotton be...

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

    SciTech Connect

    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.

  15. BAC Libraries from Wheat Chromosome 7D – Efficient Tool for Positional Cloning of Aphid Resistance Genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Positional cloning in bread wheat is a tedious task due to its huge genome size (~17 Gbp) and polyploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which make their screening very laborious. Here we pres...

  16. Construction and characterization of a human chromosome 2-specific BAC library

    SciTech Connect

    Wang, M.; Shouse, S.; Manson, J.

    1994-12-01

    We have constructed a human chromosome 2-specific bacterial artificial chromosome (BAC) library using DNA from the somatic cell hybrid GM10826. The average size of the clones is about 63 kb. The coverage and distribution of the library were estimated by screening with known polymorphic genetic markers and fluorescence in situ hybridization (FISH). Twenty-one markers tested positive when DNA pools prepared from approximately one-sixth of the library were screened with 33 known markers. This is consistent with the theoretical calculation of 63% coverage at one genomic equivalent. This suggested that the coverage of the library is approximately 5-6X. FISH analysis with 54 BACs revealed single site hybridization to chromosome 2, and the clones were distributed randomly on the chromosome. We have also performed direct sequencing of the BAC insert ends to generate sequence-tagged sites suitable for mapping and chromosome walking. This is the first reported human chromosome 2-specific BAC library and should provide a resource for physical mapping and disease searching for this chromosome. 30 refs., 5 figs.

  17. CHARACTERIZATION OF THREE MAIZE BAC LIBRARIES AND ANCHORING OF THE PHYSICAL MAP TO THE GENETIC MAP USING HIGH-DENSITY BAC FILTER HYBRIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three maize (Zea mays L.) bacterial artificial chromosome (BAC) libraries, HindIII, EcoRI and MboI, were constructed from inbred line B73 to minimize under-representation of certain genomic regions caused by the use of a single restriction enzyme library. High-density filter sets from all three lib...

  18. Development of cell lines from the sheep used to construct the CHORI-243 ovine BAC library

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two cell lines, designated MARC.OVSM and MARC.OKF, were initiated from the aorta and kidney, respectively, obtained from the Texel ram used to make the CHORI-243 Ovine BAC library. These cell lines have been submitted to the NIA Aging Cell Repository at the Coriell Cell Respositories, Camden, NJ, U...

  19. The infectious BAC genomic DNA expression library: a high capacity vector system for functional genomics.

    PubMed

    Lufino, Michele M P; Edser, Pauline A H; Quail, Michael A; Rice, Stephen; Adams, David J; Wade-Martins, Richard

    2016-01-01

    Gene dosage plays a critical role in a range of cellular phenotypes, yet most cellular expression systems use heterologous cDNA-based vectors which express proteins well above physiological levels. In contrast, genomic DNA expression vectors generate physiologically-relevant levels of gene expression by carrying the whole genomic DNA locus of a gene including its regulatory elements. Here we describe the first genomic DNA expression library generated using the high-capacity herpes simplex virus-1 amplicon technology to deliver bacterial artificial chromosomes (BACs) into cells by viral transduction. The infectious BAC (iBAC) library contains 184,320 clones with an average insert size of 134.5 kb. We show in a Chinese hamster ovary (CHO) disease model cell line and mouse embryonic stem (ES) cells that this library can be used for genetic rescue studies in a range of contexts including the physiological restoration of Ldlr deficiency, and viral receptor expression. The iBAC library represents an important new genetic analysis tool openly available to the research community. PMID:27353647

  20. The infectious BAC genomic DNA expression library: a high capacity vector system for functional genomics

    PubMed Central

    Lufino, Michele M. P.; Edser, Pauline A. H.; Quail, Michael A.; Rice, Stephen; Adams, David J.; Wade-Martins, Richard

    2016-01-01

    Gene dosage plays a critical role in a range of cellular phenotypes, yet most cellular expression systems use heterologous cDNA-based vectors which express proteins well above physiological levels. In contrast, genomic DNA expression vectors generate physiologically-relevant levels of gene expression by carrying the whole genomic DNA locus of a gene including its regulatory elements. Here we describe the first genomic DNA expression library generated using the high-capacity herpes simplex virus-1 amplicon technology to deliver bacterial artificial chromosomes (BACs) into cells by viral transduction. The infectious BAC (iBAC) library contains 184,320 clones with an average insert size of 134.5 kb. We show in a Chinese hamster ovary (CHO) disease model cell line and mouse embryonic stem (ES) cells that this library can be used for genetic rescue studies in a range of contexts including the physiological restoration of Ldlr deficiency, and viral receptor expression. The iBAC library represents an important new genetic analysis tool openly available to the research community. PMID:27353647

  1. BAC libraries of Triticum urartu, Aegilops speltoides and Ae. tauschii, the diploid ancestors of polyploid wheat.

    PubMed

    Akhunov, E D; Akhunova, A R; Dvorák, J

    2005-11-01

    Triticum urartu, Aegilops speltoides and Ae. tauschii are respectively the immediate diploid sources, or their closest relatives, of the A, B and D genomes of polyploid wheats. Here we report the construction and characterization of arrayed large-insert libraries in a bacterial artificial chromosome (BAC) vector, one for each of these diploid species. The libraries are equivalent to 3.7, 5.4 and 4.1 of the T. urartu, Ae. speltoides, Ae. tauschii genomes, respectively. The predicted levels of genome coverage were confirmed by library hybridization with single-copy genes. The libraries were used to estimate the proportion of known repeated nucleotide sequences and gene content in each genome by BAC-end sequencing. Repeated sequence families previously detected in Triticeae accounted for 57, 61 and 57% of the T. urartu, Ae. speltoides and Ae. tauschii genomes, and coding regions accounted for 5.8, 4.5 and 4.8%, respectively. PMID:16177898

  2. CHARACTERIZATION AND PHYSICAL MAPPING OF MAIZE BAC LIBRARIES USING HIGH DENSITY BAC FILTER HYBRIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-density filter sets from two maize B73 libraries containing 6X (HindIII) and 7X (EcoRI) haploid genome equivalents, respectively, were evaluated with a set of complex probes. The complex probes will provide information on chromosome architecture and organellar DNA content. A second set of pro...

  3. Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus

    SciTech Connect

    Jang Songhun; Zhou Fang; Xia Laixin; Zhao Wei; Cheng Hanhua . E-mail: hhcheng@whu.edu.cn; Zhou Rongjia . E-mail: rjzhou@whu.edu.cn

    2006-09-22

    A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes.

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

    PubMed Central

    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

  5. Enhancing genome investigations in the mosquito Culex quinquefasciatus via BAC library construction and characterization

    PubMed Central

    2011-01-01

    Background Culex quinquefasciatus (Say) is a major species in the Culex pipiens complex and an important vector for several human pathogens including West Nile virus and parasitic filarial nematodes causing lymphatic filariasis. It is common throughout tropical and subtropical regions and is among the most geographically widespread mosquito species. Although the complete genome sequence is now available, additional genomic tools are needed to improve the sequence assembly. Findings We constructed a bacterial artificial chromosome (BAC) library using the pIndigoBAC536 vector and HindIII partially digested DNA isolated from Cx. quinquefasciatus pupae, Johannesburg strain (NDJ). Insert size was estimated by NotI digestion and pulsed-field gel electrophoresis of 82 randomly selected clones. To estimate genome coverage, each 384-well plate was pooled for screening with 29 simple sequence repeat (SSR) and five gene markers. The NDJ library consists of 55,296 clones arrayed in 144 384-well microplates. Fragment insert size ranged from 50 to 190 kb in length (mean = 106 kb). Based on a mean insert size of 106 kb and a genome size of 579 Mbp, the BAC library provides ~10.1-fold coverage of the Cx. quinquefasciatus genome. PCR screening of BAC DNA plate pools for SSR loci from the genetic linkage map and for four genes associated with reproductive diapause in Culex pipiens resulted in a mean of 9.0 positive plate pools per locus. Conclusion The NDJ library represents an excellent resource for genome assembly enhancement and characterization in Culex pipiens complex mosquitoes. PMID:21914202

  6. Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

    SciTech Connect

    Venken, Koen J.T.; Carlson, Joseph W.; Schulze, Karen L.; Pan, Hongling; He, Yuchun; Spokony, Rebecca; Wan, Kenneth H.; Koriabine, Maxim; de Jong, Pieter J.; White, Kevin P.; Bellen, Hugo J.; Hoskins, Roger A.

    2009-04-21

    We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95percent of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using Phi C31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.

  7. Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2.

    PubMed

    Cação, S M B; Silva, N V; Domingues, D S; Vieira, L G E; Diniz, L E C; Vinecky, F; Alves, G S C; Andrade, A C; Carpentieri-Pipolo, V; Pereira, L F P

    2013-06-01

    Most of the world's coffee production originates from Coffea arabica, an allotetraploid species with low genetic diversity and for which few genomic resources are available. Genomic libraries with large DNA fragment inserts are useful tools for the study of plant genomes, including the production of physical maps, integration studies of physical and genetic maps, genome structure analysis and gene isolation by positional cloning. Here, we report the construction and characterization of a Bacterial Artificial Chromosome (BAC) library from C. arabica Timor Hybrid CIFC 832/2, a parental genotype for several modern coffee cultivars. The BAC library consists of 56,832 clones with an average insert size of 118 kb, which represents a dihaploid genome coverage of five to sixfold. The content of organellar DNA was estimated at 1.04 and 0.5 % for chloroplast and mitochondrial DNA, respectively. The BAC library was screened for the NADPH-dependent mannose-6-phosphate reductase gene (CaM6PR) with markers positioned on four linkage groups of a partial C. arabica genetic map. A mixed approach using PCR and membrane hybridization of BAC pools allowed for the discovery of nine BAC clones with the CaM6PR gene and 53 BAC clones that were anchored to the genetic map with simple sequence repeat markers. This library will be a useful tool for future studies on comparative genomics and the identification of genes and regulatory elements controlling major traits in this economically important crop species. PMID:23677718

  8. Construction and characterization of a Lipotes vexillifer genomic DNA BAC library.

    PubMed

    Du, Bo; Zhang, Xian-Feng; Fang, Sheng-Guo; Wang, Ding

    2007-04-01

    We constructed a genomic DNA library for Lipotes vexillifer (L. vexillifer), the Baiji or Yangtze River dolphin, one of the most endangered mammals in the world. The library consists of 149,000 BAC clones, with an average insert size of 83 kb, representing approximately 3.4 haploid genome equivalents. PCR amplification of four known L. vexillifer genes yielded two to four positive clones each. To demonstrate the utility of this library, we isolated and sequenced the L. vexillifer alpha lactalbumin gene, which is a gene specific to mammals and one which has been widely used as molecular tool in phylogenetic analysis. We also end-sequenced 20 randomly selected clones, resulting in the identification of at least five new L. vexillifer genes, five SSR loci, and one SINE locus. These results suggest that this library is a valuable resource for candidate gene cloning, physical mapping, and genome sequencing of this important and threatened species. PMID:17867838

  9. Characterization of a BAC Library from Channel Catfish Ictalurus punctatus: Indications of High Rates of Evolution Among Teleost Genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The CHORI-212 bacterial artificial chromosome (BAC) library was constructed by cloning EcoRI/EcoRI partially digested DNA into the pTARBAC2.1 vector. The library has an average insert size of 161 kb, and provides 10.6-fold coverage of the channel catfish haploid genome. Screening of 32 genes using o...

  10. Comparative genomics of Lupinus angustifolius gene-rich regions: BAC library exploration, genetic mapping and cytogenetics

    PubMed Central

    2013-01-01

    Background The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume species with a relatively compact genome. The species has 2n = 40 chromosomes and its genome size is 960 Mbp/1C. During the last decade, L. angustifolius genomic studies have achieved several milestones, such as molecular-marker development, linkage maps, and bacterial artificial chromosome (BAC) libraries. Here, these resources were integratively used to identify and sequence two gene-rich regions (GRRs) of the genome. Results The genome was screened with a probe representing the sequence of a microsatellite fragment length polymorphism (MFLP) marker linked to Phomopsis stem blight resistance. BAC clones selected by hybridization were subjected to restriction fingerprinting and contig assembly, and 232 BAC-ends were sequenced and annotated. BAC fluorescence in situ hybridization (BAC-FISH) identified eight single-locus clones. Based on physical mapping, cytogenetic localization, and BAC-end annotation, five clones were chosen for sequencing. Within the sequences of clones that hybridized in FISH to a single-locus, two large GRRs were identified. The GRRs showed strong and conserved synteny to Glycine max duplicated genome regions, illustrated by both identical gene order and parallel orientation. In contrast, in the clones with dispersed FISH signals, more than one-third of sequences were transposable elements. Sequenced, single-locus clones were used to develop 12 genetic markers, increasing the number of L. angustifolius chromosomes linked to appropriate linkage groups by five pairs. Conclusions In general, probes originating from MFLP sequences can assist genome screening and gene discovery. However, such probes are not useful for positional cloning, because they tend to hybridize to numerous loci. GRRs identified in L. angustifolius contained a low number of interspersed repeats and had a high level of synteny to the genome of the model legume G. max. Our results showed that

  11. Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins.

    PubMed

    Stevens, M R; Coleman, C E; Parkinson, S E; Maughan, P J; Zhang, H-B; Balzotti, M R; Kooyman, D L; Arumuganathan, K; Bonifacio, A; Fairbanks, D J; Jellen, E N; Stevens, J J

    2006-05-01

    Quinoa (Chenopodium quinoa Willd.) is adapted to the harsh environments of the Andean Altiplano region. Its seeds have a well-balanced amino acid composition and exceptionally high protein content with respect to human nutrition. Quinoa grain is a staple in the diet of some of the most impoverished people in the world. The plant is an allotetraploid displaying disomic inheritance (2n=4x=36) with a di-haploid genome of 967 Mbp (megabase pair), or 2C=2.01 pg. We constructed two quinoa BAC libraries using BamHI (26,880 clones) and EcoRI (48,000 clones) restriction endonucleases. Cloned inserts in the BamHI library average 113 kb (kilobase) with approximately 2% of the clones lacking inserts, whereas cloned inserts in the EcoRI library average 130 kb and approximately 1% lack inserts. Three plastid genes used as probes of high-density arrayed blots of 73,728 BACs identified approximately 2.8% of the clones as containing plastid DNA inserts. We estimate that the combined quinoa libraries represent at least 9.0 di-haploid nuclear genome equivalents. An average of 12.2 positive clones per probe were identified with 13 quinoa single-copy ESTs as probes of the high-density arrayed blots, suggesting that the estimate of 9.0x coverage of the genome is conservative. Utility of the BAC libraries for gene identification was demonstrated by probing the library with a partial sequence of the 11S globulin seed storage protein gene and identifying multiple positive clones. The presence of the 11S globulin gene in four of the clones was verified by direct comparison with quinoa genomic DNA on a Southern blot. Besides serving as a useful tool for gene identification, the quinoa BAC libraries will be an important resource for physical mapping of the quinoa genome. PMID:16586115

  12. Construction of an expressible BAC library of the unculturable insect microorganism, stink bug Plautia stali symbiont, for the search of biologically active and useful symbiont products.

    PubMed

    Kobayashi, Hideaki; Fujii-Muramatsu, Rika; Noda, Hiroaki; Takeishi, Keiichi

    2014-01-01

    While gene products and metabolites of insect symbiotic bacteria may act as useful resources for insect-microbe studies and medicinal use, it is usually difficult to obtain the insect symbionts to some extent in quantity because most of them are unculturable. In this study, the possibility of using bacterial artificial chromosome (BAC) libraries as a heterologous gene expression tool for the discovery of novel symbiont metabolites was evaluated. A BAC library was constructed from the symbiont purified from the posterior midgut cecum of the stink bug Plautia stali. The BAC library, which consisted of 513 clones with an average insert size of 41 kb, represented greater than five-fold coverage of the genome. The ability of the BAC clones to express plural genes from large-sized insert DNA in Escherichia coli was examined by the growth of BAC-transformed leu operon-deficient DH10B cells on M9 minimal medium supplemented with glucose. Two BAC clones complemented leucine deficiency in DH10B cells; the clones contained the leu operon of the symbiont chromosome. The P. stali symbiont genes introduced into the BAC vector are functional in E. coli, and these genes are expressed in an operon unit. BAC libraries can be used to generate gene product- and metabolite-libraries, facilitating to characterize potential metabolites of the P. stali symbiont. PMID:24694601

  13. Genome Enablement of the Notothenioidei: Genome Size Estimates from 11 Species and BAC Libraries from 2 Representative Taxa

    PubMed Central

    DETRICH, H. WILLIAM; STUART, ANDREW; SCHOENBORN, MICHAEL; PARKER, SANDRA K.; METHÉ, BARBARA A.; AMEMIYA, CHRIS T.

    2013-01-01

    The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species flock in the cold Southern Ocean surrounding Antarctica. To enable genome-level studies of these psychrophilic fishes, we estimated the sizes of the genomes of 11 Antarctic species and generated high-quality BAC libraries for 2, the notothen Notothenia coriiceps and the icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families, [e.g., the icefishes (Channichthyidae)], was accompanied by genome expansion. Species (n = 6) of the basal family Nototheniidae had C values that ranged between 0.98 and 1.20 pg, whereas those of the icefishes, the notothenioid crown group, were 1.66–1.83 pg (n = 4 species). The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprised 12X and 10X coverage of the respective genomes and had average insert sizes of 138 and 168 kb. Greater than 60% of paired BAC ends sampled from each library (~0.1% of each genome) contained repetitive sequences, and the repetitive element landscapes of the 2 genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The representation and depth of coverage of the libraries were verified by identification of multiple Hox gene contigs: six discrete Hox clusters were found in N. coriiceps and at least five Hox clusters were found in C. aceratus. Given the unusual anatomical and physiological adaptations of the notothenioids, the availability of these BAC libraries sets the stage for expanded analysis of the psychrophilic mode of life. PMID:20235119

  14. A BAC library of Beta vulgaris L. for the targeted isolation of centromeric DNA and molecular cytogenetics of Beta species.

    PubMed

    Jacobs, Gunnar; Dechyeva, Daryna; Wenke, Torsten; Weber, Beatrice; Schmidt, Thomas

    2009-03-01

    We constructed a sugar beet (Beta vulgaris) bacterial artificial chromosome (BAC) library of the monosomic addition line PAT2. This chromosomal mutant carries a single additional chromosome fragment (minichromosome) derived from the wild beet Beta patellaris. Restriction analysis of the mutant line by pulsed-field gel electrophoresis was used to determine HindIII as a suitable enzyme for partial digestion of genomic DNA to generate large-insert fragments which were cloned into the vector pCC1. The library consists of 36,096 clones with an average insert size of 120 kb, and 2.2% of the clones contain mitochondrial or chloroplast DNA. Based on a haploid genome size of 758 Mbp, the library represents 5.7 genome equivalents providing the probability of 99.67% that any sequence of the PAT2 genome can be found in the library. Hybridization to high-density filters was used to isolate 89 BACs containing arrays of the centromere-associated satellite repeats pTS5 and pTS4.1. Using the identified BAC clones in fluorescent in situ hybridization experiments with PAT2 and Beta patellaris chromosome spreads their wild beet origin and centromeric localization was demonstrated. Multi-colour FISH with differently labelled satellite repeats pTS5 and pTS4.1 was used to investigate the large-scale organization of the centromere of the PAT2 minichromosome in detail. FISH studies showed that the centromeric satellite pTS5 is flanked on both sides by pTS4.1 arrays and the arms of the minichromosome are terminated by the Arabidopsis-type telomeric sequences. FISH with a BAC, selected from high-density filters after hybridization with an RFLP marker of the genetic linkage group I, demonstrated that it is feasible to correlate genetic linkage groups with chromosomes. Therefore, the PAT2 BAC library provides a useful tool for the characterization of Beta centromeres and a valuable resource for sugar beet genome analysis. PMID:18386131

  15. Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L.).

    PubMed

    Liu, S Y; Yu, K; Huffner, M; Park, S J; Banik, M; Pauls, K P; Crosby, W

    2010-07-01

    A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. This source of CBB resistance is widely used in bean breeding. Several other CBB resistance QTL have been identified but none of them have been physically mapped. Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. The size of individual BAC clone inserts ranges from 30 kb to 280 kb with an average size of 107 kb. The library is estimated to represent approximately sixfold genome coverage. The BAC library was screened as BAC pools using four PCR-based molecular markers. Two to seven BAC clones were identified by each marker. Two clones were found to have both markers PV-tttc001 and STS183. One preliminary contig was assembled based on DNA finger printing of those positive BAC clones. The minimum tiling path of the contig contains 6 BAC clones spanning an estimated size of 750 kb covering the QTL region. PMID:20419470

  16. Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant.

    PubMed

    Ye, Qing; He, Ke; Wu, Shao-Ying; Wan, Qiu-Hong

    2012-01-01

    The bacterial artificial chromosome (BAC) system is widely used in isolation of large genomic fragments of interest. Construction of a routine BAC library requires several months for picking clones and arraying BACs into superpools in order to employ 4D-PCR to screen positive BACs, which might be time-consuming and laborious. The major histocompatibility complex (MHC) is a cluster of genes involved in the vertebrate immune system, and the classical avian MHC-B locus is a minimal essential one, occupying a 100-kb genomic region. In this study, we constructed a more effective reverse-4D BAC library for the golden pheasant, which first creates sub-libraries and then only picks clones of positive sub-libraries, and identified several MHC clones within thirty days. The full sequencing of a 97-kb reverse-4D BAC demonstrated that the golden pheasant MHC-B locus contained 20 genes and showed good synteny with that of the chicken. The notable differences between these two species were the numbers of class II B loci and NK genes and the inversions of the TAPBP gene and the TAP1-TAP2 region. Furthermore, the inverse TAP2-TAP1 was unique in the golden pheasant in comparison with that of chicken, turkey, and quail. The newly defined genomic structure of the golden pheasant MHC will give an insight into the evolutionary history of the avian MHC. PMID:22403630

  17. Isolation of a 97-kb Minimal Essential MHC B Locus from a New Reverse-4D BAC Library of the Golden Pheasant

    PubMed Central

    Wu, Shao-Ying; Wan, Qiu-Hong

    2012-01-01

    The bacterial artificial chromosome (BAC) system is widely used in isolation of large genomic fragments of interest. Construction of a routine BAC library requires several months for picking clones and arraying BACs into superpools in order to employ 4D-PCR to screen positive BACs, which might be time-consuming and laborious. The major histocompatibility complex (MHC) is a cluster of genes involved in the vertebrate immune system, and the classical avian MHC-B locus is a minimal essential one, occupying a 100-kb genomic region. In this study, we constructed a more effective reverse-4D BAC library for the golden pheasant, which first creates sub-libraries and then only picks clones of positive sub-libraries, and identified several MHC clones within thirty days. The full sequencing of a 97-kb reverse-4D BAC demonstrated that the golden pheasant MHC-B locus contained 20 genes and showed good synteny with that of the chicken. The notable differences between these two species were the numbers of class II B loci and NK genes and the inversions of the TAPBP gene and the TAP1-TAP2 region. Furthermore, the inverse TAP2-TAP1 was unique in the golden pheasant in comparison with that of chicken, turkey, and quail. The newly defined genomic structure of the golden pheasant MHC will give an insight into the evolutionary history of the avian MHC. PMID:22403630

  18. Development of four phylogenetically-arrayed BAC libraries and sequence of the APA locus in Phaseolus vulgaris.

    PubMed

    Kami, James; Poncet, Valérie; Geffroy, Valérie; Gepts, Paul

    2006-04-01

    The APA family of seed proteins consists of three subfamilies, in evolutionary order of hypothesized appearance: phytohaemagglutinins (PHA), alpha-amylase inhibitors (alphaAI), and arcelins (ARL). The APA family plays a defensive role against mammalian and insect seed predation in common bean (Phaseolus vulgaris L.). The main locus (APA) for this gene family is situated on linkage group B4. In order to elucidate the pattern of duplication and diversification at this locus, we developed a BAC library in each of four different Phaseolus genotypes that represent presumptive steps in the evolutionary diversification of the APA family. Specifically, BAC libraries were established in one P. lunatus (cv. 'Henderson: PHA+ alphaAI- ARL-) and three P. vulgaris accessions (presumed ancestral wild G21245 from northern Peru: PHA+ alphaAI+ ARL-; Mesoamerican wild G02771: PHA+ alphaAI+ ARL+; and Mesoamerican breeding line BAT93: PHA+ alphaAI+ ARL-). The libraries were constructed after HindIII digestion of high molecular weight DNA, obtained with a novel nuclei isolation procedure. The frequency of empty or cpDNA-sequence-containing clones in all libraries is low (generally <1%). The Henderson, G21245, and G02771 libraries have a 10x genome coverage, whereas the BAT93 library has a 20x coverage to allow further, more detailed genomic analysis of the bean genome. The complete sequence of a 155 kbp-insert clone of the G02771 library revealed six sequences belonging to the APA gene family, including members of the three subfamilies, as hypothesized. The different subfamilies were interspersed with retrotransposon sequences. In addition, other sequences were identified with similarity to chloroplast DNA, a dehydrin gene, and the Arabidopsis flowering D locus. Linkage between the dehydrin gene and the D1711 RFLP marker identifies a potential syntenic region between parts of common bean linkage group B4 and cowpea linkage group 2. PMID:16404584

  19. 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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. BAC library development, and clone characterization for dormancy-responsive DREB4A, DAM, and FT from leafy spurge (Euphorbia esula L.) identifies differential splicing and conserved promoter motifs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We developed two leafy spurge BAC libraries that together represent approximately 5X coverage of the leafy spurge genome. The BAC libraries have an average insert size of approximately 143 kb, and copies of the library and filters for hybridization-based screening are publicly available through the ...

  1. Multicolor chromosome banding (MCB) with YAC/BAC-based probes and region-specific microdissection DNA libraries

    SciTech Connect

    Liehr, T.; Weise, A.; Heller, A.; Starke, H.; Mrasek, K.; Kuechler, A.; Weier, H.-U.G.; Claussen, U.

    2003-06-23

    Multicolor chromosome banding (MCB) allows the delineation of chromosomal regions with a resolution of a few mega base pairs, i.e., slightly below the size of most visible chromosome bands. Based on the hybridization of over lapping region-specific probe libraries, chromosomal subregions are hybridized with probes that fluoresce in distinct wave length intervals, so they can be assigned predefined pseudo-colors during the digital imaging and visualization process. The present study demonstrates how MCB patterns can be produced by region-specific micro dissection derived (mcd) libraries as well as collections of yeast or bacterial artificial chromosomes (YACs and BACs, respectively). We compared the efficiency of an mcd library based approach with the hybridization of collections of locus-specific probes (LSP) for fluorescent banding of three rather differently sized human chromosomes, i.e., chromosomes 2, 13, and 22. The LSP sets were comprised of 107 probes specific for chromosome 2, 82 probes for chromosome 13, and 31 probes for chromosome 22. The results demonstrated a more homogeneous coverage of chromosomes and thus, more desirable banding patterns using the microdissection library-based MCB. This may be related to the observation that chromosomes are difficult to cover completely with YAC and/or BAC clones as single-color fluorescence in situ hybridization (FISH) experiments showed. Mcd libraries, on the other hand, provide high complexity probes that work well as region specific paints, but do not readily allow positioning of break points on genetic or physical maps as required for the positional cloning of genes. Thus, combinations of mcd libraries and locus-specific large insert DNA probes appear to be the most efficient tools for high-resolution cytogenetic analyses.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  3. Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.

    PubMed

    Magbanua, Zenaida V; Ozkan, Seval; Bartlett, Benjamin D; Chouvarine, Philippe; Saski, Christopher A; Liston, Aaron; Cronn, Richard C; Nelson, C Dana; Peterson, Daniel G

    2011-01-01

    Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb LP genome. To demonstrate the efficacy of the library in gene isolation, we screened macroarrays with overgos designed from a pine EST anchored on LP chromosome 10. A positive BAC was sequenced and found to contain the expected full-length target gene, several gene-like regions, and both known and novel repeats. Macroarray analysis using the retrotransposon IFG-7 (the most abundant repeat in the sequenced BAC) as a probe indicates that IFG-7 is found in roughly 210,557 copies and constitutes about 5.8% or 1.26 Gb of LP nuclear DNA; this DNA quantity is eight times the Arabidopsis genome. In addition to its use in genome characterization and gene isolation as demonstrated herein, the BAC library should hasten whole genome sequencing of LP via next-generation sequencing strategies/technologies and facilitate improvement of trees through molecular breeding and genetic engineering. The library and associated products are distributed by the Clemson University Genomics Institute (www.genome.clemson.edu). PMID:21283709

  4. Construction and characterization of a BAC library for the molecular dissection of a single wild beet centromere and sugar beet (Beta vulgaris) genome analysis.

    PubMed

    Gindullis, F; Dechyeva, D; Schmidt, T

    2001-10-01

    We have constructed a sugar beet bacterial artificial chromosome (BAC) library of the chromosome mutant PRO1. This Beta vulgaris mutant carries a single chromosome fragment of 6-9 Mbp that is derived from the wild beet Beta procumbens and is transmitted efficiently in meiosis and mitosis. The library consists of 50,304 clones, with an average insert size of 125 kb. Filter hybridizations revealed that approximately 3.1% of the clones contain mitochondrial or chloroplast DNA. Based on a haploid genome size of 758 Mbp, the library represents eight genome equivalents. Thus, there is a greater than 99.96% probability that any sequence of the PROI genome can be found in the library. Approximately 0.2% of the clones hybridized with centromeric sequences of the PRO1 minichromosome. Using the identified BAC clones in fluorescence in situ hybridization experiments with PRO1 and B. procumbens chromosome spreads, their wild-beet origin and centromeric localization were demonstrated. Comparative Southern hybridization of pulsed-field separated PROI DNA and BAC inserts indicate that the centromeric region of the minichromosome is represented by overlapping clones in the library. Therefore, the PRO1 BAC library provides a useful tool for the characterization of a single plant centromere and is a valuable resource for sugar beet genome analysis. PMID:11681609

  5. Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum, and the identification of clones near the late blight and Colorado potato beetle resistance loci.

    PubMed

    Chen, Q; Sun, S; Ye, Q; McCuine, S; Huff, E; Zhang, H-B

    2004-04-01

    To facilitate isolation and characterization of disease and insect resistance genes important to potato, two bacterial artificial chromosome (BAC) libraries were constructed from genomic DNA of the Mexican wild diploid species, Solanum pinnatisectum, which carries high levels of resistance to the most important potato pathogen and pest, the late blight and the Colorado potato beetle (CPB). One of the libraries was constructed from the DNA, partially digested with BamHI, and it consists of 40328 clones with an average insert size of 125 kb. The other library was constructed from the DNA partially digested with EcoRI, and it consists of 17280 clones with an average insert size of 135 kb. The two libraries, together, represent approximately six equivalents of the wild potato haploid genome. Both libraries were evaluated for contamination with organellar DNA sequences and were shown to have a very low percentage (0.65-0.91%) of clones derived from the chloroplast genome. High-density filters, prepared from the two libraries, were screened with ten restriction fragment length polymorphism (RFLP) markers linked to the resistance genes for late blight, CPB, Verticillium wilt and potato cyst nematodes, and the gene Sr1 for the self-incompatibility S-locus. Thirty nine positive clones were identified and at least two positive BAC clones were detected for each RFLP marker. Four markers that are linked to the late blight resistance gene Rpi1 hybridized to 14 BAC clones. Fifteen BAC clones were shown to harbor the PPO (polyphenol oxidase) locus for the CPB resistance by three RFLP probes. Two RFLP markers detected five BAC clones that were linked to the Sr1 gene for self-incompatibility. These results agree with the library's predicted extent of coverage of the potato genome, and indicated that the libraries are useful resources for the molecular isolation of disease and insect resistance genes, as well as other economically important genes in the wild potato species. The

  6. Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles.

    PubMed

    Shedlock, Andrew M; Janes, Daniel E; Edwards, Scott V

    2008-01-01

    Phylogenomics research integrating established principles of systematic biology and taking advantage of the wealth of DNA sequences being generated by genome science holds promise for answering long-standing evolutionary questions with orders of magnitude more primary data than in the past. Although it is unrealistic to expect whole-genome initiatives to proceed rapidly for commercially unimportant species such as reptiles, practical approaches utilizing genomic libraries of large-insert clones pave the way for a phylogenomics of species that are nevertheless essential for testing evolutionary hypotheses within a phylogenetic framework. This chapter reviews the case for adopting genome-enabled approaches to evolutionary studies and outlines a program for using bacterial artificial chromosome (BAC) libraries or plasmid libraries as a basis for completing "genome scans" of reptiles. We have used BACs to close a critical gap in the genome database for Reptilia, the sister group of mammals, and present the methodological approaches taken to achieve this as a guideline for designing similar comparative studies. In addition, we provide a detailed step-by-step protocol for BAC-library screening and shotgun sequencing of specific clones containing target genes of evolutionary interest. Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species. PMID:18629663

  7. 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

    SciTech Connect

    Mitchell, S.C.; Bocskai, D.; Cao, Y.

    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.

  8. Bac clones generated from sheared dna

    SciTech Connect

    Osoegawa, Kazutoyo; Vessere, Gery M.; Shu, Chung Li; Hoskins,Roger A.; Abad, Jose P.; de Pablos, Beatriz; Villasante, Alfredo; deJong, Pieter J.

    2006-08-09

    BAC libraries generated from restriction-digested genomic DNA display representational bias and lack some sequences. To facilitate completion of genome projects, procedures have been developed to create BACs from DNA physically sheared to create fragments extending up to 200kb. The DNA fragments were repaired to create blunt ends and ligated to a new BAC vector. This approach has been tested by generating BAC libraries from Drosophila DNA, with insert lengths of 50 kb to 150 kb. The libraries lack chimeric clone problems as determined by mapping paired BAC-end sequences of one library to the D. melanogaster genome sequence. The utility of ''sheared'' libraries was demonstrated by closure of a previous clone gap and by isolation of clones from telomeric regions, which were notably absent from previous Drosophila BAC libraries.

  9. Identification of an extensive gene cluster among a family of PPOs in Trifolium pratense L. (red clover) using a large insert BAC library

    PubMed Central

    2009-01-01

    Background Polyphenol oxidase (PPO) activity in plants is a trait with potential economic, agricultural and environmental impact. In relation to the food industry, PPO-induced browning causes unacceptable discolouration in fruit and vegetables: from an agriculture perspective, PPO can protect plants against pathogens and environmental stress, improve ruminant growth by increasing nitrogen absorption and decreasing nitrogen loss to the environment through the animal's urine. The high PPO legume, red clover, has a significant economic and environmental role in sustaining low-input organic and conventional farms. Molecular markers for a range of important agricultural traits are being developed for red clover and improved knowledge of PPO genes and their structure will facilitate molecular breeding. Results A bacterial artificial chromosome (BAC) library comprising 26,016 BAC clones with an average 135 Kb insert size, was constructed from Trifolium pratense L. (red clover), a diploid legume with a haploid genome size of 440–637 Mb. Library coverage of 6–8 genome equivalents ensured good representation of genes: the library was screened for polyphenol oxidase (PPO) genes. Two single copy PPO genes, PPO4 and PPO5, were identified to add to a family of three, previously reported, paralogous genes (PPO1–PPO3). Multiple PPO1 copies were identified and characterised revealing a subfamily comprising three variants PPO1/2, PPO1/4 and PPO1/5. Six PPO genes clustered within the genome: four separate BAC clones could be assembled onto a predicted 190–510 Kb single BAC contig. Conclusion A PPO gene family in red clover resides as a cluster of at least 6 genes. Three of these genes have high homology, suggesting a more recent evolutionary event. This PPO cluster covers a longer region of the genome than clusters detected in rice or previously reported in tomato. Full-length coding sequences from PPO4, PPO5, PPO1/5 and PPO1/4 will facilitate functional studies and provide

  10. Recombining overlapping BACs into single large BACs.

    PubMed

    Kotzamanis, George; Kotsinas, Athanassios

    2015-01-01

    BAC clones containing the entire genomic region of a gene including the long-range regulatory elements are very useful for gene functional analysis. However, large genes often span more than the insert of a BAC clone, and single BACs covering the entire region of interest are not available. Here, we describe a general system for linking two or more overlapping BACs into a single clone. Two rounds of homologous recombination are used. In the first, the BAC inserts are subcloned into the pBACLink vectors. In the second, the two BACs are combined together. Multiple BACs in a contig can be combined by alternating use of the pBACLInk vectors, resulting in several BAC clones containing as much of the genomic region of a gene as required. Such BACs can then be used in gene expression studies and/or gene therapy applications. PMID:25239744

  11. Generation of BAC-end sequences for rainbow trout genome analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For non-sequenced genomes, BAC end sequences (BES) provide a valuable sample of repetitive elements and gene content. Here we report the results of BAC end sequencing of just over half of the rainbow trout (Oncorhynchus mykiss) Swanson HindIII library. We sequenced 177,860 BAC ends that generated 17...

  12. Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity.

    PubMed

    Watson, C T; Steinberg, K M; Graves, T A; Warren, R L; Malig, M; Schein, J; Wilson, R K; Holt, R A; Eichler, E E; Breden, F

    2015-01-01

    Germline variation at immunoglobulin (IG) loci is critical for pathogen-mediated immunity, but establishing complete haplotype sequences in these regions has been problematic because of complex sequence architecture and diploid source DNA. We sequenced BAC clones from the effectively haploid human hydatidiform mole cell line, CHM1htert, across the light chain IG loci, kappa (IGK) and lambda (IGL), creating single haplotype representations of these regions. The IGL haplotype generated here is 1.25 Mb of contiguous sequence, including four novel IGLV alleles, one novel IGLC allele, and an 11.9-kb insertion. The CH17 IGK haplotype consists of two 644 kb proximal and 466 kb distal contigs separated by a large gap of unknown size; these assemblies added 49 kb of unique sequence extending into this gap. Our analysis also resulted in the characterization of seven novel IGKV alleles and a 16.7-kb region exhibiting signatures of interlocus sequence exchange between distal and proximal IGKV gene clusters. Genetic diversity in IGK/IGL was compared with that of the IG heavy chain (IGH) locus within the same haploid genome, revealing threefold (IGK) and sixfold (IGL) higher diversity in the IGH locus, potentially associated with increased levels of segmental duplication and the telomeric location of IGH. PMID:25338678

  13. BAC TransgeneOmics

    PubMed Central

    Poser, Ina; Sarov, Mihail; Hutchins, James R A; Hériché, Jean-Karim; Toyoda, Yusuke; Pozniakovsky, Andrei; Weigl, Daniela; Nitzsche, Anja; Hegemann, Björn; Bird, Alexander W; Pelletier, Laurence; Kittler, Ralf; Hua, Sujun; Naumann, Ronald; Augsburg, Martina; Sykora, Martina M; Hofemeister, Helmut; Zhang, Youming; Nasmyth, Kim; White, Kevin P; Dietzel, Steffen; Mechtler, Karl; Durbin, Richard; Stewart, A Francis; Peters, Jan-Michael; Buchholz, Frank; Hyman, Anthony A

    2009-01-01

    The interpretation of genome sequences requires reliable and standardized methods to assess protein function at high throughput. Here we describe a fast and reliable pipeline to study protein function in mammalian cells based on protein tagging in bacterial artificial chromosomes (BACs). The large size of the BAC transgenes ensures the presence of most, if not all, regulatory elements and results in expression that closely matches that of the endogenous gene. We show that BAC transgenes can be rapidly and reliably generated using 96-well-format recombineering. After stable transfection of these transgenes into human tissue culture cells or mouse embryonic stem cells, the localization, protein-protein and/or protein-DNA interactions of the tagged protein are studied using generic, tag-based assays. The same high-throughput approach will be generally applicable to other model systems. PMID:18391959

  14. Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments.

    PubMed

    Chen, Chao; Zhao, Xinqing; Jin, Yingyu; Zhao, Zongbao Kent; Suh, Joo-Won

    2014-11-01

    Bacterial artificial chromosomal (BAC) vectors are increasingly being used in cloning large DNA fragments containing complex biosynthetic pathways to facilitate heterologous production of microbial metabolites for drug development. To express inserted genes using Streptomyces species as the production hosts, an integration expression cassette is required to be inserted into the BAC vector, which includes genetic elements encoding a phage-specific attachment site, an integrase, an origin of transfer, a selection marker and a promoter. Due to the large sizes of DNA inserted into the BAC vectors, it is normally inefficient and time-consuming to assemble these fragments by routine PCR amplifications and restriction-ligations. Here we present a rapid method to insert fragments to construct BAC-based expression vectors. A DNA fragment of about 130 bp was designed, which contains upstream and downstream homologous sequences of both BAC vector and pIB139 plasmid carrying the whole integration expression cassette. In-Fusion cloning was performed using the designer DNA fragment to modify pIB139, followed by λ-RED-mediated recombination to obtain the BAC-based expression vector. We demonstrated the effectiveness of this method by rapid construction of a BAC-based expression vector with an insert of about 120 kb that contains the entire gene cluster for biosynthesis of immunosuppressant FK506. The empty BAC-based expression vector constructed in this study can be conveniently used for construction of BAC libraries using either microbial pure culture or environmental DNA, and the selected BAC clones can be directly used for heterologous expression. Alternatively, if a BAC library has already been constructed using a commercial BAC vector, the selected BAC vectors can be manipulated using the method described here to get the BAC-based expression vectors with desired gene clusters for heterologous expression. The rapid construction of a BAC-based expression vector facilitates

  15. The first report of a Pelecaniformes defensin cluster: characterization of β-defensin genes in the crested ibis based on BAC libraries.

    PubMed

    Lan, Hong; Chen, Hui; Chen, Li-Cheng; Wang, Bei-Bing; Sun, Li; Ma, Mei-Ying; Fang, Sheng-Guo; Wan, Qiu-Hong

    2014-01-01

    Defensins play a key role in the innate immunity of various organisms. Detailed genomic studies of the defensin cluster have only been reported in a limited number of birds. Herein, we present the first characterization of defensins in a Pelecaniformes species, the crested ibis (Nipponia nippon), which is one of the most endangered birds in the world. We constructed bacterial artificial chromosome libraries, including a 4D-PCR library and a reverse-4D library, which provide at least 40 equivalents of this rare bird's genome. A cluster including 14 β-defensin loci within 129 kb was assigned to chromosome 3 by FISH, and one gene duplication of AvBD1 was found. The ibis defensin genes are characterized by multiform gene organization ranging from two to four exons through extensive exon fusion. Splicing signal variations and alternative splice variants were also found. Comparative analysis of four bird species identified one common and multiple species-specific duplications, which might be associated with high GC content. Evolutionary analysis revealed birth-and-death mode and purifying selection for avian defensin evolution, resulting in different defensin gene numbers among bird species and functional conservation within orthologous genes, respectively. Additionally, we propose various directions for further research on genetic conservation in the crested ibis. PMID:25372018

  16. A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization

    PubMed Central

    2009-01-01

    Background Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian. Results The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. NotI digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole). Conclusion We have demonstrated the utility of the

  17. Generation of BAC reporter cell lines for drug discovery.

    PubMed

    Kao, Betty R; McColl, Bradley; Vadolas, Jim

    2015-01-01

    Bacterial artificial chromosome (BAC) reporter cell lines are generated through stable transfection of a BAC reporter construct wherein the gene of interest is tagged with a reporter gene such as eGFP. The large capacity of BACs (up to 350 kb of genomic sequence) enables the inclusion of all regulatory elements that ensure appropriate regulation of the gene of interest. Furthermore, the reporter gene allows the expression of the gene of interest to be readily detected by flow cytometry. Cell lines can also be easily cultured for extended periods with minimal cost. These features of BAC reporter cell lines make them highly amenable for use in high-throughput screening of large drug libraries for compounds that induce the expression of the gene of interest. This chapter describes a method for generation of BAC reporter cell lines that are suitable as cellular assay systems in high-throughput screening. Briefly, this method involves (A) generation of cell clones stably transfected with a BAC reporter construct, (B) selection of "candidate" cell clones based on the responsiveness to known inducers, (C) confirmation of the integrity of the BAC reporter construct integrated within the candidate clones, and (D) assessment of the developmental regulation of the BAC reporter construct. As an example, we describe the generation of a BAC reporter cell line containing the human β-globin locus modified to express γ-globin as eGFP for use as a cellular reporter assay for screening of drugs that can reactivate expression of developmentally silenced γ-globin for the treatment of β-hemoglobin disorders. PMID:25239756

  18. Localization and Characterization of 170 BAC-derived clones and mapping of Ninety-Four Microsatellites in the Hessian Fly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ninety-four microsatellites from enriched genomic libraries of Hessian fly (Mayetiola destructor (Say)) were localized to 170 cognate clones in a Hessian fly bacterial artificial chromosome (BAC) library. These microsatellite-positive BAC clones were physically mapped to polytene chromosomes by fl...

  19. BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A bacterial artificial chromosome (BAC) library and BAC-end sequences for Gossypium hirsutum L. have recently been developed. Here we report on genomic-based genome-wide SNP mining utilizing re-sequencing data with a BAC-end sequence reference for twelve G. hirsutum L. lines, one G. barbadense L. li...

  20. Characterizing the walnut genome through analyses of BAC end sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Persian walnut (Juglans regia L.) is an economically important tree for its nut crop and timber. To gain insight into the structure and evolution of the walnut genome, we constructed two bacterial artificial chromosome (BAC) libraries, containing a total of 129,024 clones, from in vitro-grown shoots...

  1. Screening and chromosome localization of two cotton BAC clones.

    PubMed

    Cui, Xinglei; Liu, Fang; Liu, Yuling; Zhou, Zhongli; Wang, Chunying; Yanyan Zhao; Meng, Fei; Wang, Xingxing; Cai, Xiaoyan; Wang, Yuhong; Peng, Renhai; Wang, Kunbo

    2016-01-01

    Two bacterial artificial chromosome (BAC) clones (350B21 and 299N22) of Pima 90-53 cotton [Gossypium barbadense Linnaeus, 1753 (2n=4x=52)] were screened from a BAC library using SSR markers. Strong hybridization signals were detected at terminal regions of all A genome (sub-genome) chromosomes, but were almost absent in D genome (sub-genome) chromosomes with BAC clone 350B21 as the probe. The results indicate that specific sequences, which only exist at the terminal parts of A genome (sub-genome) chromosomes with a huge repeat number, may be contained in BAC clone 350B21. When utilizing FISH with the BAC clone 299N22 as probe, a pair of obvious signals was detected on chromosome 13 of D genome (sub-genome), while strong dispersed signals were detected on all A genome (sub-genome) chromosomes. The results showed that peculiar repetitive sequence, which was distributed throughout all A genome (sub-genome) chromosomes, may exist in BAC clone 299N22. The absence of the repetitive sequences, which exist in the two BAC clones, in D genome may account for the genome-size variation between A and D genomes. In addition, the microcolinearity analysis of the clone 299N22 and its homologous region on Gossypium raimondii Ulbrich, 1932 chromosome 13 (D513) indicated that the clone 299N22 might come from A sub-genome of sea island cotton (Gossypium barbadense), and a huge number of small deletions, illegitimate recombination, translocation and rearrangements may have occurred during the genus evolution. The two BAC clones studied here can be used as cytological markers but will be also be helpful to research in cotton genome evolution and comparative genomics. PMID:27186333

  2. Screening and chromosome localization of two cotton BAC clones

    PubMed Central

    Cui, Xinglei; Liu, Fang; Liu, Yuling; Zhou, Zhongli; Wang, Chunying; Yanyan Zhao; Meng, Fei; Wang, Xingxing; Cai, Xiaoyan; Wang, Yuhong; Peng, Renhai; Wang, Kunbo

    2016-01-01

    Abstract Two bacterial artificial chromosome (BAC) clones (350B21 and 299N22) of Pima 90-53 cotton [Gossypium barbadense Linnaeus, 1753 (2n=4x=52)] were screened from a BAC library using SSR markers. Strong hybridization signals were detected at terminal regions of all A genome (sub-genome) chromosomes, but were almost absent in D genome (sub-genome) chromosomes with BAC clone 350B21 as the probe. The results indicate that specific sequences, which only exist at the terminal parts of A genome (sub-genome) chromosomes with a huge repeat number, may be contained in BAC clone 350B21. When utilizing FISH with the BAC clone 299N22 as probe, a pair of obvious signals was detected on chromosome 13 of D genome (sub-genome), while strong dispersed signals were detected on all A genome (sub-genome) chromosomes. The results showed that peculiar repetitive sequence, which was distributed throughout all A genome (sub-genome) chromosomes, may exist in BAC clone 299N22. The absence of the repetitive sequences, which exist in the two BAC clones, in D genome may account for the genome-size variation between A and D genomes. In addition, the microcolinearity analysis of the clone 299N22 and its homologous region on Gossypium raimondii Ulbrich, 1932 chromosome 13 (D513) indicated that the clone 299N22 might come from A sub-genome of sea island cotton (Gossypium barbadense), and a huge number of small deletions, illegitimate recombination, translocation and rearrangements may have occurred during the genus evolution. The two BAC clones studied here can be used as cytological markers but will be also be helpful to research in cotton genome evolution and comparative genomics. PMID:27186333

  3. Library+

    ERIC Educational Resources Information Center

    Merrill, Alex

    2011-01-01

    This article discusses possible future directions for academic libraries in the post Web/Library 2.0 world. These possible directions include areas such as data literacy, linked data sets, and opportunities for libraries in support of digital humanities. The author provides a brief sketch of the background information regarding the topics and…

  4. BAC-Pool Sequencing and Assembly of 19 Mb of the Complex Sugarcane Genome.

    PubMed

    Okura, Vagner Katsumi; de Souza, Rafael S C; de Siqueira Tada, Susely F; Arruda, Paulo

    2016-01-01

    Sequencing plant genomes are often challenging because of their complex architecture and high content of repetitive sequences. Sugarcane has one of the most complex genomes. It is highly polyploid, preserves intact homeologous chromosomes from its parental species and contains >55% repetitive sequences. Although bacterial artificial chromosome (BAC) libraries have emerged as an alternative for accessing the sugarcane genome, sequencing individual clones is laborious and expensive. Here, we present a strategy for sequencing and assembly reads produced from the DNA of pooled BAC clones. A set of 178 BAC clones, randomly sampled from the SP80-3280 sugarcane BAC library, was pooled and sequenced using the Illumina HiSeq2000 and PacBio platforms. A hybrid assembly strategy was used to generate 2,451 scaffolds comprising 19.2 MB of assembled genome sequence. Scaffolds of ≥20 Kb corresponded to 80% of the assembled sequences, and the full sequences of forty BACs were recovered in one or two contigs. Alignment of the BAC scaffolds with the chromosome sequences of sorghum showed a high degree of collinearity and gene order. The alignment of the BAC scaffolds to the 10 sorghum chromosomes suggests that the genome of the SP80-3280 sugarcane variety is ∼19% contracted in relation to the sorghum genome. In conclusion, our data show that sequencing pools composed of high numbers of BAC clones may help to construct a reference scaffold map of the sugarcane genome. PMID:27047520

  5. BAC-Pool Sequencing and Assembly of 19 Mb of the Complex Sugarcane Genome

    PubMed Central

    Okura, Vagner Katsumi; de Souza, Rafael S. C.; de Siqueira Tada, Susely F.; Arruda, Paulo

    2016-01-01

    Sequencing plant genomes are often challenging because of their complex architecture and high content of repetitive sequences. Sugarcane has one of the most complex genomes. It is highly polyploid, preserves intact homeologous chromosomes from its parental species and contains >55% repetitive sequences. Although bacterial artificial chromosome (BAC) libraries have emerged as an alternative for accessing the sugarcane genome, sequencing individual clones is laborious and expensive. Here, we present a strategy for sequencing and assembly reads produced from the DNA of pooled BAC clones. A set of 178 BAC clones, randomly sampled from the SP80-3280 sugarcane BAC library, was pooled and sequenced using the Illumina HiSeq2000 and PacBio platforms. A hybrid assembly strategy was used to generate 2,451 scaffolds comprising 19.2 MB of assembled genome sequence. Scaffolds of ≥20 Kb corresponded to 80% of the assembled sequences, and the full sequences of forty BACs were recovered in one or two contigs. Alignment of the BAC scaffolds with the chromosome sequences of sorghum showed a high degree of collinearity and gene order. The alignment of the BAC scaffolds to the 10 sorghum chromosomes suggests that the genome of the SP80-3280 sugarcane variety is ∼19% contracted in relation to the sorghum genome. In conclusion, our data show that sequencing pools composed of high numbers of BAC clones may help to construct a reference scaffold map of the sugarcane genome. PMID:27047520

  6. Making BAC transgene constructs with lambda-red recombineering system for transgenic animals or cell lines.

    PubMed

    Holmes, Scott; Lyman, Suzanne; Hsu, Jen-Kang; Cheng, JrGang

    2015-01-01

    The genomic DNA libraries based on Bacteria Artificial Chromosomes (BAC) are the foundation of whole genomic mapping, sequencing, and annotation for many species like mice and humans. With their large insert size, BACs harbor the gene-of-interest and nearby transcriptional regulatory elements necessary to direct the expression of the gene-of-interest in a temporal and cell-type specific manner. When replacing a gene-of-interest with a transgene in vivo, the transgene can be expressed with the same patterns and machinery as that of the endogenous gene. This chapter describes in detail a method of using lambda-red recombineering to make BAC transgene constructs with the integration of a transgene into a designated location within a BAC. As the final BAC construct will be used for transfection in cell lines or making transgenic animals, specific considerations with BAC transgenes such as genotyping, BAC coverage and integrity as well as quality of BAC DNA will be addressed. Not only does this approach provide a practical and effective way to modify large DNA constructs, the same recombineering principles can apply to smaller high copy plasmids as well as to chromosome engineering. PMID:25239742

  7. SEQUENCING THE PIG GENOME USING A BAC BY BAC APPROACH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have generated a highly contiguous physical map covering >98% of the pig genome in just 176 contigs. The map is localized to the genome through integration with the UIVC RH map as well BAC end sequence alignments to the human genome. Over 265k HindIII restriction digest fingerprints totaling 16.2...

  8. Effects of Blood-Alcohol Concentration (BAC) Feedback on BAC Estimates Over Time

    ERIC Educational Resources Information Center

    Bullers, Susan; Ennis, Melissa

    2006-01-01

    This study examines the effects of self-tested blood alcohol concentration (BAC) feedback, from personal hand-held breathalyzers, on the accuracy of BAC estimation. Using an e-mail prompted web-based questionnaire, 19 participants were asked to report both BAC estimates and subsequently measured BAC levels over the course of 27 days. Results from…

  9. BAC sequencing using pooled methods.

    PubMed

    Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

    2015-01-01

    Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly. PMID:25239741

  10. Recombineering-Based Procedure for Creating BAC Transgene Constructs for Animals and Cell Lines

    PubMed Central

    Hollenback, Steven M.; Lyman, Suzanne; Cheng, JrGang

    2011-01-01

    The use of BAC/P1 as a vector for the generation of a transgene has gained popularity after the genomic annotation of many organisms was completed (often based on the respective BAC library). Large-scale generation of BAC transgenic mice has proven that BAC transgene approaches have less integration position effects and dosage artifacts when compared with traditional transgenic approaches. Also, a BAC can achieve the same tissue-specific expression as a Knock-in of the same gene with less effort and shorter time of establishment. The λ-RED recombinogenic system has been used to manipulate DNA constructs with site-directed mutagenesis, truncation, and tagging with an epitope tag or as a fusion protein by homologous recombination, as well as used here to modify many BACs with various transgenes. The recombineering plasmid, pKD46, is used to fabricate BAC transgenic constructs that can be used in generating transgenic organisms as well as used in mammalian cell culture. PMID:21732318

  11. A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurata L.)

    PubMed Central

    Kuhl, Heiner; Sarropoulou, Elena; Tine, Mbaye; Kotoulas, Georgios; Magoulas, Antonios; Reinhardt, Richard

    2011-01-01

    This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata), a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp). Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus) genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome. PMID:21049003

  12. Construction and characterization of a human bacterial artificial chromosome library

    SciTech Connect

    Kim, Ung-Jin; Birren, B.W.; Slepak, T.

    1996-06-01

    We have constructed an arrayed human genomic BAC library with approximately 4X coverage that is represented by 96,000 BAC clones with average insert size of nearly 140 kb. A new BAC vector that allows color-based positive screening to identify transformants with inserts has increased BAC cloning efficiency. The library was gridded onto hybridization filters at high density for efficient identification of BAC clones by colony hybridization. The library was also formulated into characteristic DNA pools to allow for PCR screening of the library mainly by screening with more than 300 different landmarks that include cDNA, STSs, and cosmid clones. We describe methods for using BAC clones and discuss the implications for genome characterization, mapping, and sequencing. 25 refs., 5 figs., 1 tab.

  13. A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2.

    PubMed

    Cao, Y; Kang, H L; Xu, X; Wang, M; Dho, S H; Huh, J R; Lee, B J; Kalush, F; Bocskai, D; Ding, Y; Tesmer, J G; Lee, J; Moon, E; Jurecic, V; Baldini, A; Weier, H U; Doggett, N A; Simon, M I; Adams, M D; Kim, U J

    1999-08-01

    We have constructed a complete coverage BAC contig map that spans a 12-Mb genomic segment in the human chromosome 16p13.1-p11.2 region. The map consists of 68 previously mapped STSs and 289 BAC clones, 51 of which-corresponding to a total of 7.721 Mb of genomic DNA-have been sequenced, and provides a high resolution physical map of the region. Contigs were initially built based mainly on the analysis of STS contents and restriction fingerprint patterns of the clones. To close the gaps, probes derived from BAC clone ends were used to screen deeper BAC libraries. Clone end sequence data obtained from chromosome 16-specific BACs, as well as from public databases, were used for the identification of BACs that overlap with fully sequenced BACs by means of sequence match. This approach allowed precise alignment of clone overlaps in addition to restriction fingerprint comparison. A freehand contig drawing software tool was developed and used to manage the map data graphically and generate a real scale physical map. The map we present here is approximately 3.5 x deep and provides a minimal tiling path that covers the region in an array of contigous, overlapping BACs. PMID:10447511

  14. Construction and characterization of a bacterial artificial chromosome library for hexaploid wheat line 92R137

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sub libraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was compos...

  15. Distribution of Genes and Repetitive Elements in the Diabrotica virgifera virgifera Genome Estimated Using BAC Sequencing

    PubMed Central

    Coates, Brad S.; Alves, Analiza P.; Wang, Haichuan; Walden, Kimberly K. O.; French, B. Wade; Miller, Nicholas J.; Abel, Craig A.; Robertson, Hugh M.; Sappington, Thomas W.; Siegfried, Blair D.

    2012-01-01

    Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104 ± 34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage) and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding. PMID:22919272

  16. Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing.

    PubMed

    Coates, Brad S; Alves, Analiza P; Wang, Haichuan; Walden, Kimberly K O; French, B Wade; Miller, Nicholas J; Abel, Craig A; Robertson, Hugh M; Sappington, Thomas W; Siegfried, Blair D

    2012-01-01

    Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104 ± 34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage) and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding. PMID:22919272

  17. A First Generation BAC Physical Map of the Rainbow Trout Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physical map was constructed using the high-information content fingerprinting (HICF) method of Luo et al. (2003; Genomics, 82, 378-389). All the clones from the Swanson YY doubled haploid male BAC library (10X coverage; 184,704 clones) were fingerprinted and edited using FPMiner software. App...

  18. Herpesvirus BACs: Past, Present, and Future

    PubMed Central

    Warden, Charles; Tang, Qiyi; Zhu, Hua

    2011-01-01

    The herpesviridae are a large family of DNA viruses with large and complicated genomes. Genetic manipulation and the generation of recombinant viruses have been extremely difficult. However, herpesvirus bacterial artificial chromosomes (BACs) that were developed approximately 10 years ago have become useful and powerful genetic tools for generating recombinant viruses to study the biology and pathogenesis of herpesviruses. For example, BAC-directed deletion mutants are commonly used to determine the function and essentiality of viral genes. In this paper, we discuss the creation of herpesvirus BACs, functional analyses of herpesvirus mutants, and future applications for studies of herpesviruses. We describe commonly used methods to create and mutate herpesvirus BACs (such as site-directed mutagenesis and transposon mutagenesis). We also evaluate the potential future uses of viral BACs, including vaccine development and gene therapy. PMID:21048927

  19. Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH.

    PubMed

    Vasconcelos, Emanuelle Varão; de Andrade Fonsêca, Artur Fellipe; Pedrosa-Harand, Andrea; de Andrade Bortoleti, Kyria Cilene; Benko-Iseppon, Ana Maria; da Costa, Antônio Félix; Brasileiro-Vidal, Ana Christina

    2015-06-01

    Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes. PMID:25634499

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

    SciTech Connect

    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.

  1. Directing enhancer-traps and iTol2 end-sequences to deleted BAC ends with loxP- and lox511-Tn10 transposons.

    PubMed

    Chatterjee, Pradeep K

    2015-01-01

    A step-by-step detailed procedure is presented to progressively truncate genomic DNA inserts from either end in BACs. The bacterial transposon Tn10 carrying a loxP or a lox511 site is inserted at random into BAC DNA inside the bacterial cell. The cells are then infected with bacteriophage P1. The Cre protein expressed by phage P1 generates end-deletions by specifically recombining the inserted loxP (or lox511) with the loxP (or lox511) endogenous to and flanking insert DNA in BACs from the respective end. The Cre protein also helps phage P1 transduce the BAC DNA by packaging it in P1 heads. This packaging by P1 not only recovers the rare BAC clones containing Tn10 insertions efficiently but also selects end-truncated BACs from those containing inversions of portions of their DNA caused by transposition of Tn10 in the opposite orientation. The libraries of end-deleted BACs generated by this procedure are suitable for numerous mapping studies. Because DNA in front of the loxP (or lox511) arrowheads in the Tn10 transposon is retained at the newly created BAC end, exogenous DNA cassettes such as enhancer-traps and iTol2 ends can be efficiently introduced into BAC ends for germline expression in zebrafish or mice. The methodology should facilitate functional mapping studies of long-range cis-acting gene regulatory sequences in these organisms. PMID:25239743

  2. Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones.

    PubMed

    Taboada, Xoana; Pansonato-Alves, Jose C; Foresti, Fausto; Martínez, Paulino; Viñas, Ana; Pardo, Belén G; Bouza, Carmen

    2014-06-01

    Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly. PMID:24473579

  3. BacDive—the Bacterial Diversity Metadatabase

    PubMed Central

    Söhngen, Carola; Bunk, Boyke; Podstawka, Adam; Gleim, Dorothea; Overmann, Jörg

    2014-01-01

    BacDive—the Bacterial Diversity Metadatabase (http://bacdive.dsmz.de) merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. Currently (release 9/2013), BacDive contains entries for 23 458 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. Where available, links to access the respective biological resources are given. The majority of the BacDive data is manually annotated and curated. The BacDive portal offers an easy-to-use simple search and in addition powerful advanced search functionalities allowing to combine more than 30 search fields for text and numerical data. The user can compile individual sets of strains to a download selection that can easily be imported into nearly all spreadsheet applications. PMID:24214959

  4. BacDive--the Bacterial Diversity Metadatabase.

    PubMed

    Söhngen, Carola; Bunk, Boyke; Podstawka, Adam; Gleim, Dorothea; Overmann, Jörg

    2014-01-01

    BacDive-the Bacterial Diversity Metadatabase (http://bacdive.dsmz.de) merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. Currently (release 9/2013), BacDive contains entries for 23 458 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. Where available, links to access the respective biological resources are given. The majority of the BacDive data is manually annotated and curated. The BacDive portal offers an easy-to-use simple search and in addition powerful advanced search functionalities allowing to combine more than 30 search fields for text and numerical data. The user can compile individual sets of strains to a download selection that can easily be imported into nearly all spreadsheet applications. PMID:24214959

  5. Recombineering BAC transgenes for protein tagging.

    PubMed

    Ciotta, Giovanni; Hofemeister, Helmut; Maresca, Marcello; Fu, Jun; Sarov, Mihail; Anastassiadis, Konstantinos; Stewart, A Francis

    2011-02-01

    Protein tagging offers many advantages for proteomic and regulomic research, particularly due to the use of generic and highly sensitive methods that can be applied with reasonable throughput. Ideally, protein tagging is equivalent to having a high affinity antibody for every chosen protein. However, these advantages are compromised if the tagged protein is overexpressed, which is usually the case from cDNA expression vectors. BAC (bacterial artificial chromosome) transgenes present a way to express a chosen protein at physiological levels with all regulatory elements in their native configurations, including cell cycle, alternative splicing and microRNA regulation. Recombineering has become the method of choice for modifying large constructs like BACs. Here, we present a method for protein tagging by recombineering BACs, transfecting cells and evaluating tagged protein expression. PMID:20868752

  6. Toward a Molecular Cytogenetic Map for Cultivated Sunflower (Helianthus annuus L.) by Landed BAC/BIBAC Clones

    PubMed Central

    Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

    2013-01-01

    Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (∼100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC- fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)−derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources. PMID:23316437

  7. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.

    PubMed

    Paux, Etienne; Legeai, Fabrice; Guilhot, Nicolas; Adam-Blondon, Anne-Françoise; Alaux, Michaël; Salse, Jérôme; Sourdille, Pierre; Leroy, Philippe; Feuillet, Catherine

    2008-02-01

    Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes. PMID:18038165

  8. A Multiway Analysis for Identifying High Integrity Bovine BACs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In large genomics projects involving many different types of analyses of bacterial artificial chromosomes (BACs), such as fingerprinting, end sequencing (BES) and full BAC sequencing there are many opportunities for the identities of BACs to become confused. However, by comparing the results from t...

  9. SplinkBES - A Splinkerette-Based Method for Generating Long End Sequences From Large Insert DNA Libraries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report on the development of a novel splinkerette-based method for generating long end-sequences from large insert library clones, using a carrot (Daucus carota L.) BAC library as a model. The procedure involves digestion of the BAC DNA with a 6-bp restriction enzyme, followed by ligation of spli...

  10. SweetBac: Applying MultiBac Technology Towards Flexible Modification of Insect Cell Glycosylation.

    PubMed

    Palmberger, Dieter; Rendic, Dubravko

    2015-01-01

    Observed different glycosylation patterns of glycoconjugates (recombinantly) produced in various eukaryotic organisms are a direct consequence of differences in numerous proteins involved in biosynthesis of the relevant glycan chains in these species. The need for efficient, robust and flexible methods for recombinant expression of proteins is met by the recently described MultiBac technology, an advanced and optimized baculovirus-based system for simultaneous recombinant protein expression in insect cells. A derivative of MultiBac technology, the SweetBac system aims at the modification of the glycosylation potential of insect cells as expression hosts. The application of SweetBac, including the methods needed to investigate the glycosylation pattern of the purified recombinant protein, is described in this chapter. PMID:26082221

  11. Improved method for high-efficiency electrotransformation of Escherichia coli with the large BAC plasmids.

    PubMed

    Nováková, Jana; Izsáková, Anita; Grivalský, Tomáš; Ottmann, Christian; Farkašovský, Marian

    2014-01-01

    High transformation competency of Escherichia coli is one of the critical factors in the bacterial artificial chromosome (BAC)-based DNA library construction. Many electroporation protocols have been published until now, but the majority of them was optimized for transformation of small plasmids. Large plasmids with a size above 50 kbp display reduced transformation efficiency and thereby require specific conditions in the preparation and electroporation of electrocompetent cells. In the present work, we have optimized the parameters critical to the application of BAC DNA electrotransformation into E. coli. Systematic evaluation of electroporation variables has revealed several key factors like temperature of growth, media supplements, washing buffer, and cell concentration. Improvements made in the transformation protocol have led to electrocompetent cells with transformation efficiency up to 7 × 10(8) transformants per microgram of 120 kbp BAC plasmid DNA. We have successfully used in-house prepared competent cells, the quality of which is comparable with those produced by different companies, in the construction of metagenomic libraries from the soil. Our protocol can also be beneficial for other application with limited DNA source. PMID:23846555

  12. [Advanced Treatment of Incineration Leachate with O3-BAC and Double O3-BAC].

    PubMed

    Du, An-jing; Fan, Ju-hong; Liu, Rui; Qiu, Song-kai; Wen, Xiao-gang; Chen, Lü-jun

    2015-11-01

    Ozone-biological activated carbon (O3-BAC) process and double O3-BAC process were respectively used for advanced treatment of the biologically treated effluent of incineration leachate, and their pollutant removal performances were compared. The results showed that the double O3-BAC removed 75.9% ± 2.1% of chemical oxygen demand (COD), 78.8% ± 2.9% of UV254 and 96.8% ± 0.9% of color at ozone dosage of 200 mg x L(-1). The treated effluent was with COD of below 100 mg x L(-1) and color of below 40 times, meeting the emission requirements of GB 16889-2008. At the same ozone dosage, however, the O3-BAC removed 68.2% ± 1.3% of COD, 69.7% ± 0.5% of UV254 and 92.5% ± 1.1% of color. The treated effluent was with COD of around 150 mg x L(-1) and color of about 60 times, failing to meet the emission requirements. Namely, ozone of 290 mg x L(-1) was required by O3-BAC in order to achieve similar pollutant removals as those in double O3-BAC at O3 dosage of 200 mg x L(-1). In double O3-BAC at ozone dosage of 200 mg x L(-1), total phosphorus was removed by 63.5% ± 4.4%, and the phosphorus concentration in the effluent was remained 1 mg x L(-1) or less, directly meeting the emission requirement of GB 16889-2008. PMID:26911003

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

    PubMed Central

    Woo, S S; Jiang, J; Gill, B S; Paterson, A H; Wing, R A

    1994-01-01

    The construction of representative large insert DNA libraries is critical for the analysis of complex genomes. The predominant vector system for such work is the yeast artificial chromosome (YAC) system. Despite the success of YACs, many problems have been described including: chimerism, tedious steps in library construction and low yields of YAC insert DNA. Recently a new E.coli based system has been developed, the bacterial artificial chromosome (BAC) system, which offers many potential advantages over YACs. We tested the BAC system in plants by constructing an ordered 13,440 clone sorghum BAC library. The library has a combined average insert size, from single and double size selections, of 157 kb. Sorghum inserts of up to 315 kb were isolated and shown to be stable when grown for over 100 generations in liquid media. No chimeric clones were detected as determined by fluorescence in situ hybridization of ten BAC clones to metaphase and interphase S.bicolor nuclei. The library was screened with six sorghum probes and three maize probes and all but one sorghum probe hybridized to at least one BAC clone in the library. To facilitate chromosome walking with the BAC system, methods were developed to isolate the proximal ends of restriction fragments inserted into the BAC vector and used to isolate both the left and right ends of six randomly selected BAC clones. These results demonstrate that the S. bicolor BAC library will be useful for several physical mapping and map-based cloning applications not only in sorghum but other related cereal genomes, such as maize. Furthermore, we conclude that the BAC system is suitable for most large genome applications, is more 'user friendly' than the YAC system, and will likely lead to rapid progress in cloning biologically significant genes from plants. Images PMID:7800481

  14. [Construction and analysis of rumen bacterial artificial chromosome library from a dairy cow rumen microflora].

    PubMed

    Zhu, Ya-xin; Wang, Jia-qi; Ma, Run-lin; Huang, Li; Dong, Zhi-yang

    2007-04-01

    The high molecular weight DNA was extracted and purified directly from rumen samples in the study by using culture-independent and pulsed field gel electrophoresis approaches. After digestion with Hind III, DNA fragments ranging from 50-100 kb was collected and ligated to pCC BAC vector. The ligation mixture was transformed into E. coli EPI300 and a rumen metagenomic BAC library with about 15360 clones was constructed. The average insert size is about 54.5 kb, mostly ranging from 50-70 kb, and the capacity of this BAC library is about 837Mb. Several BAC clones with activity of amylase, Cmcellulase had been screened from the BAC library. The clones with Cmcelluase activity were screened further for linchenase, xylanase, cellobioase activity and the result is that 25 of them have at least one kind of other enzyme activity. PMID:17552222

  15. Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

    PubMed Central

    2010-01-01

    Background Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has a high intra-specific genetic variation, morphologic diversity and a small genome size (454 Mb), which make it suitable for a great variety of molecular and genetic studies. A number of genetic and genomic resources have already been developed, such as several genetic maps, BAC genomic libraries, a BAC-based physical map and EST collections. Sequence information would be invaluable to complete the picture of the melon genomic landscape, furthering our understanding of this species' evolution from its relatives and providing an important genetic tool. However, to this day there is little sequence data available, only a few melon genes and genomic regions are deposited in public databases. The development of massively parallel sequencing methods allows envisaging new strategies to obtain long fragments of genomic sequence at higher speed and lower cost than previous Sanger-based methods. Results In order to gain insight into the structure of a significant portion of the melon genome we set out to perform massive sequencing of pools of BAC clones. For this, a set of 57 BAC clones from a double haploid line was sequenced in two pools with the 454 system using both shotgun and paired-end approaches. The final assembly consists of an estimated 95% of the actual size of the melon BAC clones, with most likely complete sequences for 50 of the BACs, and a total sequence coverage of 39x. The accuracy of the assembly was assessed by comparing the previously available Sanger sequence of one of the BACs against its 454 sequence, and the polymorphisms found involved only 1.7 differences every 10,000 bp that were localized in 15 homopolymeric regions and two dinucleotide tandem repeats. Overall, the study provides approximately 6.7 Mb or 1.5% of the melon genome. The analysis of this new data has allowed us to gain further

  16. Fungicidal mechanisms of the antimicrobial peptide Bac8c.

    PubMed

    Lee, Wonyoung; Lee, Dong Gun

    2015-02-01

    Bac8c (RIWVIWRR-NH2) is an analogue peptide derived through complete substitution analysis of the linear bovine host defense peptide variant Bac2A. In the present study, the antifungal mechanism of Bac8c against pathogenic fungi was investigated, with a particular focus on the effects of Bac8c on the cytoplasmic membrane. We used bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC4(3)] staining and 3,3'-dipropylthiacarbocyanine iodide [DiSC3(5)] assays to show that Bac8c induced disturbances in the membrane potential of Candida albicans. An increase in membrane permeability and suppression of cell wall regeneration were also observed in Bac8c-treated C. albicans. We studied the effects of Bac8c treatment on model membranes to elucidate its antifungal mechanism. Using calcein and FITC-labeled dextran leakage assays from Bac8c-treated large unilamellar vesicles (LUVs) and giant unilamellar vesicles (GUVs), we found that Bac8c has a pore-forming action on fungal membranes, with an estimated pore radius of between 2.3 and 3.3 nm. A membrane-targeted mechanism of action was also supported by the observation of potassium release from the cytosol of Bac8c-treated C. albicans. These results indicate that Bac8c is considered as a potential candidate to develop a novel antimicrobial agent because of its low-cost production characteristics and high antimicrobial activity via its ability to induce membrane perturbations in fungi. PMID:25434926

  17. BAC to the future: functional genomics in mammals

    PubMed Central

    Roguev, Assen; Krogan, Nevan J

    2012-01-01

    A high-throughput pipeline to engineer bacterial artificial chromosomes (BACs) expressing tagged genes of higher eukaryotes allows large-scale protein localization and interaction studies. PMID:18446155

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

    PubMed

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

    2014-01-01

    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. PMID:24608928

  19. Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

    PubMed Central

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

    2014-01-01

    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. PMID:24608928

  20. Sequencing the Pig Genome Using a Mapped BAC by BAC Approach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have generated a highly contiguous physical map covering >98% of the pig genome in just 176 contigs. The map is localised to the genome through integration with the UIUC RH map as well BAC end sequence alignments to the human genome. Over 265k HindIII restriction digest fingerprints totalling 1...

  1. Generation of BAC Transgenic Epithelial Organoids

    PubMed Central

    Schwank, Gerald; Andersson-Rolf, Amanda; Koo, Bon-Kyoung; Sasaki, Nobuo; Clevers, Hans

    2013-01-01

    Under previously developed culture conditions, mouse and human intestinal epithelia can be cultured and expanded over long periods. These so-called organoids recapitulate the three-dimensional architecture of the gut epithelium, and consist of all major intestinal cell types. One key advantage of these ex vivo cultures is their accessibility to live imaging. So far the establishment of transgenic fluorescent reporter organoids has required the generation of transgenic mice, a laborious and time-consuming process, which cannot be extended to human cultures. Here we present a transfection protocol that enables the generation of recombinant mouse and human reporter organoids using BAC (bacterial artificial chromosome) technology. PMID:24204693

  2. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Oryza Map Alignment Project (OMAP) provides the first comprehensive experimental system for understanding the evolution, physiology and biochemistry of a full genus in plants or animals. We have constructed twelve deep-coverage BAC libraries that are representative of both diploid and tetraploid...

  3. Generation of bacterial artificial chromosome (BAC) transgenic mice.

    PubMed

    Beil, Jane; Buch, Thorsten

    2014-01-01

    Transgenic mice are among the most helpful tools to study the role of genes in physiological conditions. In this protocol, we describe the generation of bacterial artificial chromosome (BACs) constructs, which are used to express a gene of interest under a particular promoter. BACs as driver of transgenes have the advantage that a characterization of transcriptional control elements is unnecessary and the construct's size usually reduces position effects from random integration. In the following, we firstly explain in detail the amplification of the BAC, the generation of the targeting construct as well as the recombination by ET-cloning, and the analysis of the recombined clones by Southern blot analysis. Finally, we also describe the preparation of the BACs for oocyte injection. In total, the construction of such BAC transgenes needs around 6-8 weeks. PMID:25064102

  4. BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

    NASA Astrophysics Data System (ADS)

    Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

    2012-05-01

    Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

  5. Olefin Isomerization Regiochemistries during Tandem Action of BacA and BacB on Prephenate in Bacilysin Biosynthesis†

    PubMed Central

    Parker, Jared B.; Walsh, Christopher T.

    2012-01-01

    BacA and BacB, the first two enzymes of the bacilysin pathway, convert prephenate to an exocylic regioisomer of dihydrohydroxyphenylpyruvate (ex-H2HPP) on the way to the epoxycyclohexanone warhead in the dipeptide antibiotic, bacilysin. BacA decarboxylates prephenate without aromatization, converting the 1,4-diene in prephenate to the endocyclic 1,3 diene in Δ4Δ8-dihydrohydroxyphenylpyruvate (en-H2HPP). BacB then performs an allylic isomerization to bring the diene into conjugation with the 2-ketone in the product Δ3Δ5-dihydrohydroxyphenylpyruvate (ex-H2HPP). To prove that BacA acts regiospecifically on one of the two prochiral olefins in prephenate, we generated 1,5,8-[13C]-chorismate from bacterial fermentation of 5-[13C]-glucose and in turn produced 2,4,6-[13C]-prephenate via chorismate mutase. Tandem action of BacA and BacB gave 2,4,8-[13C]-7R-ex-H2HPP, showing that BacA isomerizes only the pro-R double bond in prephenate. Nonenzymatic isomerization of the BacA product into conjugation gives only the Δ3 E-geometric isomer of Δ3Δ5-ex-H2HPP. On the other hand, acceleration of the allylic isomerization by BacB gives a mixture of the E- and Z-geometric isomers of the 7R-product, indicating some rerouting of the flux, likely through dienolate geometric isomers. PMID:22483065

  6. Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project.

    PubMed

    Park, Tae-Ho; Park, Beom-Seok; Kim, Jin-A; Hong, Joon Ki; Jin, Mina; Seol, Young-Joo; Mun, Jeong-Hwan

    2011-01-01

    As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome (BAC) by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa. PMID:21338952

  7. Construction, characterization and FISH mapping of a bacterial artificial chromosome library of Chinese pangolin (Manis pentadactyla).

    PubMed

    Che, J; Wang, J; Su, W; Ye, J; Wang, Y; Nie, W; Yang, F

    2008-01-01

    Chinese pangolins as a representative species in the order Pholidota have highly specified morphological characters and occupy an important place in the mammalian phylogenetic tree. To obtain genomic data for this species, we have constructed a bacterial artificial chromosome (BAC) library of Chinese pangolin. The library contains 208,272 clones with an average insert size of 122.1 kb and represents approximately eight times the Chinese pangolin haploid genome (if we assume that the Chinese pangolins have a genome size similar to human). One hundred and twenty randomly-selected BAC clones were mapped onto Chinese pangolin chromosomes by fluorescence in situ hybridization (FISH), showing a largely unbiased chromosomal distribution. Several clones containing repetitive DNA and ribosomal DNA genes were also found. The BAC library and FISH mapped BAC clones are useful resources for comparative genomics and cytogenetics of mammals and in particular, the ongoing genome sequencing project of Chinese pangolins. PMID:18931486

  8. Genome-wide end-sequenced BAC resources for the NOD/MrkTac☆ and NOD/ShiLtJ☆☆ mouse genomes

    PubMed Central

    Steward, Charles A.; Humphray, Sean; Plumb, Bob; Jones, Matthew C.; Quail, Michael A.; Rice, Stephen; Cox, Tony; Davies, Rob; Bonfield, James; Keane, Thomas M.; Nefedov, Michael; de Jong, Pieter J.; Lyons, Paul; Wicker, Linda; Todd, John; Hayashizaki, Yoshihide; Gulban, Omid; Danska, Jayne; Harrow, Jen; Hubbard, Tim; Rogers, Jane; Adams, David J.

    2010-01-01

    Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes (T1D) due to the progressive loss of insulin-secreting β-cells by an autoimmune driven process. NOD mice represent a valuable tool for studying the genetics of T1D and for evaluating therapeutic interventions. Here we describe the development and characterization by end-sequencing of bacterial artificial chromosome (BAC) libraries derived from NOD/MrkTac (DIL NOD) and NOD/ShiLtJ (CHORI-29), two commonly used NOD substrains. The DIL NOD library is composed of 196,032 BACs and the CHORI-29 library is composed of 110,976 BACs. The average depth of genome coverage of the DIL NOD library, estimated from mapping the BAC end-sequences to the reference mouse genome sequence, was 7.1-fold across the autosomes and 6.6-fold across the X chromosome. Clones from this library have an average insert size of 150 kb and map to over 95.6% of the reference mouse genome assembly (NCBIm37), covering 98.8% of Ensembl mouse genes. By the same metric, the CHORI-29 library has an average depth over the autosomes of 5.0-fold and 2.8-fold coverage of the X chromosome, the reduced X chromosome coverage being due to the use of a male donor for this library. Clones from this library have an average insert size of 205 kb and map to 93.9% of the reference mouse genome assembly, covering 95.7% of Ensembl genes. We have identified and validated 191,841 single nucleotide polymorphisms (SNPs) for DIL NOD and 114,380 SNPs for CHORI-29. In total we generated 229,736,133 bp of sequence for the DIL NOD and 121,963,211 bp for the CHORI-29. These BAC libraries represent a powerful resource for functional studies, such as gene targeting in NOD embryonic stem (ES) cell lines, and for sequencing and mapping experiments. PMID:19909804

  9. Bacterial Artificial Chromosome Libraries of Pulse Crops: Characteristics and Applications

    PubMed Central

    Yu, Kangfu

    2012-01-01

    Pulse crops are considered minor on a global scale despite their nutritional value for human consumption. Therefore, they are relatively less extensively studied in comparison with the major crops. The need to improve pulse crop production and quality will increase with the increasing global demand for food security and people's awareness of nutritious food. The improvement of pulse crops will require fully utilizing all their genetic resources. Bacterial artificial chromosome (BAC) libraries of pulse crops are essential genomic resources that have the potential to accelerate gene discovery and enhance molecular breeding in these crops. Here, we review the availability, characteristics, applications, and potential applications of the BAC libraries of pulse crops. PMID:21811383

  10. Expression of Functional Recombinant Human Tissue Transglutaminase (TG2) Using the Bac-to-Bac Baculovirus Expression System

    PubMed Central

    Yazdani, Yaghoub; Azari, Shahram; Kalhor, Hamid Reza

    2016-01-01

    Purpose: Tissue transglutaminase (TG2) is a unique multifunctional enzyme. The enzyme possesses enzymatic activities such as transamidation/crosslinking and non-enzymatic functions such as cell migration and signal transduction. TG2 has been shown to be involved in molecular mechanisms of cancers and several neurodegenerative diseases such as Alzheimer’s disease. The present study aimed at cloning and expression of full length human TG2 in Bac-to-Bac baculovirus expression system and evaluation of its activity. Methods: pFastBac HTA donor vector containing coding sequence of human TG2 was constructed. The construct was transformed to DH10Bac for generating recombinant bacmid. The verified bacmid was transfected to insect cell line (Sf9). Expression of recombinant TG2 was examined by RT-PCR, SDS-PAGE and western blot analysis. Functional analysis was evaluated by fluorometric assay and gel electrophoresis. Results: Recombinant bacmid was verified by amplification of a band near to 4500 bp. Expression analysis showed that the enzyme was expressed as a protein with a molecular weight near 80 kDa. Western blot confirmed the presence of TG2 and the activity assays including flurometric assay indicated that the recombinant TG2 was functional. The electrophoresis assay conformed that the expressed TG2 was the indeed capable of crosslinking in the presence of physiological concentration calcium ions. Conclusion: Human TG2 was expressed efficiently in the active biological form in the Bac-to-Bac baculovirus expression system. The expressed enzyme could be used for medical diagnostic, or studies which aim at finding novel inhibitors of the enzymes . To best of our knowledge, this is probably the first report of expression of full length human tissue transglutaminase (TG2) using the Bac-to-Bac expression system. PMID:27123417

  11. Losing Libraries, Saving Libraries

    ERIC Educational Resources Information Center

    Miller, Rebecca

    2010-01-01

    This summer, as public libraries continued to get budget hit after budget hit across the country, several readers asked for a comprehensive picture of the ravages of the recession on library service. In partnership with 2010 Movers & Shakers Laura Solomon and Mandy Knapp, Ohio librarians who bought the Losing Libraries domain name, "LJ" launched…

  12. Construction, complete sequence, and annotation of a BAC contig covering the silkworm chorion locus.

    PubMed

    Chen, Zhiwei; Nohata, Junko; Guo, Huizhen; Li, Shenglong; Liu, Jianqiu; Guo, Youbing; Yamamoto, Kimiko; Kadono-Okuda, Keiko; Liu, Chun; Arunkumar, Kallare P; Nagaraju, Javaregowda; Zhang, Yan; Liu, Shiping; Labropoulou, Vassiliki; Swevers, Luc; Tsitoura, Panagiota; Iatrou, Kostas; Gopinathan, Karumathil P; Goldsmith, Marian R; Xia, Qingyou; Mita, Kazuei

    2015-01-01

    The silkmoth chorion was studied extensively by F.C. Kafatos' group for almost 40 years. However, the complete structure of the chorion locus was not obtained in the genome sequence of Bombyx mori published in 2008 due to repetitive sequences, resulting in gaps and an incomplete view of the locus. To obtain the complete sequence of the chorion locus, expressed sequence tags (ESTs) derived from follicular epithelium cells were used as probes to screen a bacterial artificial chromosome (BAC) library. Seven BACs were selected to construct a contig which covered the whole chorion locus. By Sanger sequencing, we successfully obtained complete sequences of the chorion locus spanning 871,711 base pairs on chromosome 2, where we annotated 127 chorion genes. The dataset reported here will recruit more researchers to revisit one of the oldest model systems which has been used to study developmentally regulated gene expression. It also provides insights into egg development and fertilization mechanisms and is relevant to applications related to improvements in breeding procedures and transgenesis. PMID:26594380

  13. Construction, complete sequence, and annotation of a BAC contig covering the silkworm chorion locus

    PubMed Central

    Chen, Zhiwei; Nohata, Junko; Guo, Huizhen; Li, Shenglong; Liu, Jianqiu; Guo, Youbing; Yamamoto, Kimiko; Kadono-Okuda, Keiko; Liu, Chun; Arunkumar, Kallare P.; Nagaraju, Javaregowda; Zhang, Yan; Liu, Shiping; Labropoulou, Vassiliki; Swevers, Luc; Tsitoura, Panagiota; Iatrou, Kostas; Gopinathan, Karumathil P.; Goldsmith, Marian R.; Xia, Qingyou; Mita, Kazuei

    2015-01-01

    The silkmoth chorion was studied extensively by F.C. Kafatos’ group for almost 40 years. However, the complete structure of the chorion locus was not obtained in the genome sequence of Bombyx mori published in 2008 due to repetitive sequences, resulting in gaps and an incomplete view of the locus. To obtain the complete sequence of the chorion locus, expressed sequence tags (ESTs) derived from follicular epithelium cells were used as probes to screen a bacterial artificial chromosome (BAC) library. Seven BACs were selected to construct a contig which covered the whole chorion locus. By Sanger sequencing, we successfully obtained complete sequences of the chorion locus spanning 871,711 base pairs on chromosome 2, where we annotated 127 chorion genes. The dataset reported here will recruit more researchers to revisit one of the oldest model systems which has been used to study developmentally regulated gene expression. It also provides insights into egg development and fertilization mechanisms and is relevant to applications related to improvements in breeding procedures and transgenesis. PMID:26594380

  14. Comparative Analysis of piggyBac, CRISPR/Cas9 and TALEN Mediated BAC Transgenesis in the Zygote for the Generation of Humanized SIRPA Rats.

    PubMed

    Jung, Chris J; Ménoret, Séverine; Brusselle, Lucas; Tesson, Laurent; Usal, Claire; Chenouard, Vanessa; Remy, Séverine; Ouisse, Laure-Hélène; Poirier, Nicolas; Vanhove, Bernard; de Jong, Pieter J; Anegon, Ignacio

    2016-01-01

    BAC transgenic mammalian systems offer an important platform for recapitulating human gene expression and disease modeling. While the larger body mass, and greater genetic and physiologic similarity to humans render rats well suited for reproducing human immune diseases and evaluating therapeutic strategies, difficulties of generating BAC transgenic rats have hindered progress. Thus, an efficient method for BAC transgenesis in rats would be valuable. Immunodeficient mice carrying a human SIRPA transgene have previously been shown to support improved human cell hematopoiesis. Here, we have generated for the first time, human SIRPA BAC transgenic rats, for which the gene is faithfully expressed, functionally active, and germline transmissible. To do this, human SIRPA BAC was modified with elements to work in coordination with genome engineering technologies-piggyBac, CRISPR/Cas9 or TALEN. Our findings show that piggyBac transposition is a more efficient approach than the classical BAC transgenesis, resulting in complete BAC integration with predictable end sequences, thereby permitting precise assessment of the integration site. Neither CRISPR/Cas9 nor TALEN increased BAC transgenesis. Therefore, an efficient generation of human SIRPA transgenic rats using piggyBac opens opportunities for expansion of humanized transgenic rat models in the future to advance biomedical research and therapeutic applications. PMID:27530248

  15. Comparative Analysis of piggyBac, CRISPR/Cas9 and TALEN Mediated BAC Transgenesis in the Zygote for the Generation of Humanized SIRPA Rats

    PubMed Central

    Jung, Chris J.; Ménoret, Séverine; Brusselle, Lucas; Tesson, Laurent; Usal, Claire; Chenouard, Vanessa; Remy, Séverine; Ouisse, Laure-Hélène; Poirier, Nicolas; Vanhove, Bernard; de Jong, Pieter J.; Anegon, Ignacio

    2016-01-01

    BAC transgenic mammalian systems offer an important platform for recapitulating human gene expression and disease modeling. While the larger body mass, and greater genetic and physiologic similarity to humans render rats well suited for reproducing human immune diseases and evaluating therapeutic strategies, difficulties of generating BAC transgenic rats have hindered progress. Thus, an efficient method for BAC transgenesis in rats would be valuable. Immunodeficient mice carrying a human SIRPA transgene have previously been shown to support improved human cell hematopoiesis. Here, we have generated for the first time, human SIRPA BAC transgenic rats, for which the gene is faithfully expressed, functionally active, and germline transmissible. To do this, human SIRPA BAC was modified with elements to work in coordination with genome engineering technologies-piggyBac, CRISPR/Cas9 or TALEN. Our findings show that piggyBac transposition is a more efficient approach than the classical BAC transgenesis, resulting in complete BAC integration with predictable end sequences, thereby permitting precise assessment of the integration site. Neither CRISPR/Cas9 nor TALEN increased BAC transgenesis. Therefore, an efficient generation of human SIRPA transgenic rats using piggyBac opens opportunities for expansion of humanized transgenic rat models in the future to advance biomedical research and therapeutic applications. PMID:27530248

  16. BAC transgenesis in human embryonic stem cells as a novel tool to define the human neural lineage.

    PubMed

    Placantonakis, Dimitris G; Tomishima, Mark J; Lafaille, Fabien; Desbordes, Sabrina C; Jia, Fan; Socci, Nicholas D; Viale, Agnes; Lee, Hyojin; Harrison, Neil; Tabar, Viviane; Studer, Lorenz

    2009-03-01

    Human embryonic stem cells (hESCs) have enormous potential for applications in basic biology and regenerative medicine. However, harnessing the potential of hESCs toward generating homogeneous populations of specialized cells remains challenging. Here we describe a novel technology for the genetic identification of defined hESC-derived neural cell types using bacterial artificial chromosome (BAC) transgenesis. We generated hESC lines stably expressing Hes5::GFP, Dll1::GFP, and HB9::GFP BACs that yield green fluorescent protein (GFP)(+) neural stem cells, neuroblasts, and motor neurons, respectively. Faithful reporter expression was confirmed by cell fate analysis and appropriate transgene regulation. Prospective isolation of HB9::GFP(+) cells yielded purified human motor neurons with proper marker expression and electrophysiological activity. Global mRNA and microRNA analyses of Hes5::GFP(+) and HB9::GFP(+) populations revealed highly specific expression signatures, suggesting that BAC transgenesis will be a powerful tool for establishing expression libraries that define the human neural lineage and for accessing defined cell types in applications of human disease. PMID:19074416

  17. Establishment of the BacMam system using silkworm baculovirus.

    PubMed

    Imai, Atsutoshi; Tadokoro, Takashi; Kita, Shunsuke; Horiuchi, Masataka; Fukuhara, Hideo; Maenaka, Katsumi

    2016-09-16

    The BacMam system uses modified insect viruses (baculoviruses) as vehicles to efficiently deliver genes for expression in mammalian cells. The technique can be widely applied to large-scale recombinant protein production with appropriate modifications, high-throughput screening platforms for cell-based assays, and the delivery of large genes. The silkworm system is often employed as a rapid and cost-effective approach for recombinant baculovirus generation. Here we have developed the novel BacMam system using silkworm baculovirus, and shown the successful expression of EGFP in mammalian cells. The transduction to mammalian cells via the BacMam system was improved by adding phosphate-buffered saline and sodium butyrate to the culture medium and lowering the temperature after viral infection. This study provides an alternative gene delivery system for mammalian cells, which has various potential applications, including efficient native protein production and gene therapy. PMID:27480929

  18. BacMet: antibacterial biocide and metal resistance genes database

    PubMed Central

    Pal, Chandan; Bengtsson-Palme, Johan; Rensing, Christopher; Kristiansson, Erik; Larsson, D. G. Joakim

    2014-01-01

    Antibiotic resistance has become a major human health concern due to widespread use, misuse and overuse of antibiotics. In addition to antibiotics, antibacterial biocides and metals can contribute to the development and maintenance of antibiotic resistance in bacterial communities through co-selection. Information on metal and biocide resistance genes, including their sequences and molecular functions, is, however, scattered. Here, we introduce BacMet (http://bacmet.biomedicine.gu.se)—a manually curated database of antibacterial biocide- and metal-resistance genes based on an in-depth review of the scientific literature. The BacMet database contains 470 experimentally verified resistance genes. In addition, the database also contains 25 477 potential resistance genes collected from public sequence repositories. All resistance genes in the BacMet database have been organized according to their molecular function and induced resistance phenotype. PMID:24304895

  19. BacDive--The Bacterial Diversity Metadatabase in 2016.

    PubMed

    Söhngen, Carola; Podstawka, Adam; Bunk, Boyke; Gleim, Dorothea; Vetcininova, Anna; Reimer, Lorenz Christian; Ebeling, Christian; Pendarovski, Cezar; Overmann, Jörg

    2016-01-01

    BacDive-the Bacterial Diversity Metadatabase (http://bacdive.dsmz.de) provides strain-linked information about bacterial and archaeal biodiversity. The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. The majority of data is manually annotated and curated. Currently (with release 9/2015), BacDive covers 53 978 strains. Newly implemented RESTful web services provide instant access to the content in machine-readable XML and JSON format. Besides an overall increase of data content, BacDive offers new data fields and features, e.g. the search for gene names, plasmids or 16S rRNA in the advanced search, as well as improved linkage of entries to external life science web resources. PMID:26424852

  20. BAC transgenic zebrafish for transcriptional promoter and enhancer studies.

    PubMed

    Kraus, Petra; Winata, Cecilia L; Lufkin, Thomas

    2015-01-01

    With the advent of BAC recombineering techniques, transcriptional promoter and enhancer isolation studies have become much more feasible in zebrafish than in mouse given the easy access to large numbers of fertilized zebrafish eggs and offspring in general, the easy to follow ex-utero development of zebrafish, an overall less skill demand and a more cost-effective technique. Here we provide guidelines for the generation of BAC recombineering-based transgenic zebrafish for DNA transcriptional promoter and enhancer identification studies as well as protocols for their analysis, which have been successfully applied in our laboratories many times. BAC recombineering in zebrafish allows for economical functional genomics studies, for example by integrating developmental biology with comparative genomics approaches to validate potential enhancer elements of vertebrate transcription factors. PMID:25239750

  1. An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

    PubMed Central

    2011-01-01

    Background Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding. Results We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes) of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species. Conclusion Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive DNA and SSR markers

  2. Characterizing a novel strain of Bacillus amyloliquefaciens BAC03 for potential biological control application

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: Identify and characterize a bacterial strain from suppressive soil, BAC03, evaluate its antimicrobial activity against Streptomyces scabies and other microorganisms, and characterize an antimicrobial substance produced by this strain. Methods and Results: Bacterial strain BAC03 (isolated from ...

  3. As Blood Alcohol Content (BAC) Increases, So Does Impairment | NIH MedlinePlus the Magazine

    MedlinePlus

    ... on. Feature: Rethinking Drinking As Blood Alcohol Content (BAC) Increases, So Does Impairment Past Issues / Spring 2014 ... For purposes of law enforcement, blood alcohol content (BAC) is used to define intoxication and provides a ...

  4. Construction and targeted retrieval of specific clone from a non-gridded soybean bacterial artificial chromosome library.

    PubMed

    Xia, Zhengjun; Wu, Hongyan; Watanabe, Satoshi; Harada, Kyuya

    2014-01-01

    Although a post-genomic era is emerging for many plants, the bacterial artificial chromosome (BAC) library is still a valuable tool for genomic studies and preservation of precious genetic resources. Construction of non-gridded BAC libraries would dramatically reduce cost and save storage space. A non-gridded BAC library composed of approximately 96,000 insert-containing clones in 80 pools with an average insert size of 75 kb was constructed. This library represented 5.2 genome equivalents. We successfully developed a unique procedure to retrieve positive clones from the non-gridded pools. With this retrieving protocol, the non-gridded library system can be adapted to different species and to serve various research needs. PMID:24090869

  5. TAL effectors mediate high-efficiency transposition of the piggyBac transposon in silkworm Bombyx mori L

    PubMed Central

    Ye, Lupeng; You, Zhengying; Qian, Qiujie; Zhang, Yuyu; Che, Jiaqian; Song, Jia; Zhong, Boxiong

    2015-01-01

    The piggyBac (PB) transposon is one of the most useful transposable elements, and has been successfully used for genetic manipulation in more than a dozen species. However, the efficiency of PB-mediated transposition is still insufficient for many purposes. Here, we present a strategy to enhance transposition efficiency using a fusion of transcription activator-like effector (TALE) and the PB transposase (PBase). The results demonstrate that the TALE-PBase fusion protein which is engineered in this study can produce a significantly improved stable transposition efficiency of up to 63.9%, which is at least 7 times higher than the current transposition efficiency in silkworm. Moreover, the average number of transgene-positive individuals increased up to 5.7-fold, with each positive brood containing an average of 18.1 transgenic silkworms. Finally, we demonstrate that TALE-PBase fusion-mediated PB transposition presents a new insertional preference compared with original insertional preference. This method shows a great potential and value for insertional therapy of many genetic diseases. In conclusion, this new and powerful transposition technology will efficiently promote genetic manipulation studies in both invertebrates and vertebrates. PMID:26608076

  6. Library Cooperation.

    ERIC Educational Resources Information Center

    Lund, Patricia; And Others

    1993-01-01

    Includes nine articles that discuss cooperative library networking in Illinois. Highlights include library systems as cooperative agencies; PALI (Private Academic Libraries of Illinois); rural school and public library development; systemwide users; regional medical libraries; virtual libraries and the Coalition for Networked Information; a…

  7. BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

    PubMed Central

    Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Stoffel, Kevin; Zheng, Xiuting; Saski, Christopher A.; Scheffler, Brian E.; Fang, David D.; Chen, Z. Jeffrey; Van Deynze, Allen; Stelly, David M.

    2015-01-01

    A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies. PMID:25858960

  8. BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping.

    PubMed

    Hulse-Kemp, Amanda M; Ashrafi, Hamid; Stoffel, Kevin; Zheng, Xiuting; Saski, Christopher A; Scheffler, Brian E; Fang, David D; Chen, Z Jeffrey; Van Deynze, Allen; Stelly, David M

    2015-06-01

    A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies. PMID:25858960

  9. Separation of homologous BAC contigs in the tetraploid Upland cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Upland cotton has an allotetraploid genome. Separation of homologous BAC contigs to their sub-genomes and further to individual chromosomes is a great challenge for genome-wide integrated genetic and physical mapping. As a pilot experiment to test the feasibility of separating the contigs in sub-g...

  10. Bacteriocin Protein BacL1 of Enterococcus faecalis Is a Peptidoglycan d-Isoglutamyl-l-lysine Endopeptidase*

    PubMed Central

    Kurushima, Jun; Hayashi, Ikue; Sugai, Motoyuki; Tomita, Haruyoshi

    2013-01-01

    Enterococcus faecalis strains are commensal bacteria in humans and other animals, and they are also the causative agent of opportunistic infectious diseases. Bacteriocin 41 (Bac41) is produced by certain E. faecalis clinical isolates, and it is active against other E. faecalis strains. Our genetic analyses demonstrated that the extracellular products of the bacL1 and bacA genes, which are encoded in the Bac41 operon, coordinately express the bacteriocin activity against E. faecalis. In this study, we investigated the molecular functions of the BacL1 and BacA proteins. Immunoblotting and N-terminal amino acid sequence analysis revealed that BacL1 and BacA are secreted without any processing. The coincidental treatment with the recombinant BacL1 and BacA showed complete bacteriocin activity against E. faecalis, but neither BacL1 nor BacA protein alone showed the bacteriocin activity. Interestingly, BacL1 alone demonstrated substantial degrading activity against the cell wall fraction of E. faecalis in the absence of BacA. Furthermore, MALDI-TOF MS analysis revealed that BacL1 has a peptidoglycan d-isoglutamyl-l-lysine endopeptidase activity via a NlpC/P60 homology domain. These results collectively suggest that BacL1 serves as a peptidoglycan hydrolase and, when BacA is present, results in the lysis of viable E. faecalis cells. PMID:24235140

  11. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens.

    PubMed

    Wang, Congli; Ulloa, Mauricio; Shi, Xinyi; Yuan, Xiaohui; Saski, Christopher; Yu, John Z; Roberts, Philip A

    2015-01-01

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) are foci for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode (Meloidogyne incognita), reniform nematode (Rotylenchulus reniformis), Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum), Verticillium wilt (Verticillium dahliae), and black root rot (Thielaviopsis basicola). Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences, plus 146 (Chr 11) and 98 (Chr 21) predicted genes. GO functional profiling of Unigenes uncovered genes involved in different metabolic functions and stress response elements (SRE). Our results revealed that Chrs 11 and 21 harbor resistance gene rich genomic regions. Sequence comparisons with the ancestral diploid D5 (G. raimondii), A2 (G. arboreum) and domesticated tetraploid TM-1 AD1 (G. hirsutum) genomes revealed abundance of transposable elements and confirmed the richness of resistance gene motifs in these chromosomes. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes and breeding for resistance to cotton diseases. PMID

  12. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens

    PubMed Central

    Wang, Congli; Ulloa, Mauricio; Shi, Xinyi; Yuan, Xiaohui; Saski, Christopher; Yu, John Z.; Roberts, Philip A.

    2015-01-01

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) are foci for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode (Meloidogyne incognita), reniform nematode (Rotylenchulus reniformis), Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum), Verticillium wilt (Verticillium dahliae), and black root rot (Thielaviopsis basicola). Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences, plus 146 (Chr 11) and 98 (Chr 21) predicted genes. GO functional profiling of Unigenes uncovered genes involved in different metabolic functions and stress response elements (SRE). Our results revealed that Chrs 11 and 21 harbor resistance gene rich genomic regions. Sequence comparisons with the ancestral diploid D5 (G. raimondii), A2 (G. arboreum) and domesticated tetraploid TM-1 AD1 (G. hirsutum) genomes revealed abundance of transposable elements and confirmed the richness of resistance gene motifs in these chromosomes. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes and breeding for resistance to cotton diseases. PMID

  13. Construction and characterization of three wheat bacterial artificial chromosome libraries.

    PubMed

    Cao, Wenjin; Fu, Bisheng; Wu, Kun; Li, Na; Zhou, Yan; Gao, Zhongxia; Lin, Musen; Li, Guoqiang; Wu, Xinyi; Ma, Zhengqiang; Jia, Haiyan

    2014-01-01

    We have constructed three bacterial artificial chromosome (BAC) libraries of wheat cultivar Triticum aestivum Wangshuibai, germplasms T. monococcum TA2026 and TA2033. A total of 1,233,792,170,880 and 263,040 clones were picked and arrayed in 384-well plates. On the basis of genome sizes of 16.8 Gb for hexaploid wheat and 5.6 Gb for diploid wheat, the three libraries represented 9.05-, 2.60-, and 3.71-fold coverage of the haploid genomes, respectively. An improved descending pooling system for BAC libraries screening was established. This improved strategy can save 80% of the time and 68% of polymerase chain reaction (PCR) with the same successful rate as the universal 6D pooling strategy. PMID:25464379

  14. Construction and Characterization of Three Wheat Bacterial Artificial Chromosome Libraries

    PubMed Central

    Cao, Wenjin; Fu, Bisheng; Wu, Kun; Li, Na; Zhou, Yan; Gao, Zhongxia; Lin, Musen; Li, Guoqiang; Wu,  Xinyi; Ma, Zhengqiang; Jia, Haiyan

    2014-01-01

    We have constructed three bacterial artificial chromosome (BAC) libraries of wheat cultivar Triticum aestivum Wangshuibai, germplasms T. monococcum TA2026 and TA2033. A total of 1,233,792,170,880 and 263,040 clones were picked and arrayed in 384-well plates. On the basis of genome sizes of 16.8 Gb for hexaploid wheat and 5.6 Gb for diploid wheat, the three libraries represented 9.05-, 2.60-, and 3.71-fold coverage of the haploid genomes, respectively. An improved descending pooling system for BAC libraries screening was established. This improved strategy can save 80% of the time and 68% of polymerase chain reaction (PCR) with the same successful rate as the universal 6D pooling strategy. PMID:25464379

  15. BacT/Alert: an automated colorimetric microbial detection system.

    PubMed Central

    Thorpe, T C; Wilson, M L; Turner, J E; DiGuiseppi, J L; Willert, M; Mirrett, S; Reller, L B

    1990-01-01

    BacT/Alert (Organon Teknika Corp., Durham, N.C.) is an automated microbial detection system based on the colorimetric detection of CO2 produced by growing microorganisms. Results of an evaluation of the media, sensor, detection system, and detection algorithm indicate that the system reliably grows and detects a wide variety of bacteria and fungi. Results of a limited pilot clinical trial with a prototype research instrument indicate that the system is comparable to the radiometric BACTEC 460 system in its ability to grow and detect microorganisms in blood. On the basis of these initial findings, large-scale clinical trials comparing BacT/Alert with other commercial microbial detection systems appear warranted. PMID:2116451

  16. Removal of Inserted BAC after linearizatiON (RIBON)-a novel strategy to excise the mini-F sequences from viral BAC vectors.

    PubMed

    Ishihara, Yukari; Esaki, Motoyuki; Yasuda, Atsushi

    2016-08-01

    The bacterial artificial chromosome (BAC) technology has been a mainstay approach for generating recombinant viruses, and several methods for excision of the mini-F sequences from the viral BAC vectors have been developed. However, these strategies either require complicated procedures or leave scars of inserted sequences. To overcome these problems, a new method to excise the mini-F sequences from viral BAC vectors based on the Removal of Inserted BAC after linearizatiON (RIBON) strategy was developed in this study for herpesvirus of turkeys (HVT). Enhanced green fluorescent protein (eGFP) DNA and the mini-F sequences were inserted into the gene encoding HVT thymidine kinase (TK) by homologous recombination in chicken embryo fibroblasts (CEFs), and the constructed HVT-BAC vector was used to transform Escherichia coli (pHVT-BAC). To remove the inserted eGFP and mini-F sequences, pHVT-BAC was linearized using a homing endonuclease I-SceI and used to cotransfect CEFs together with a plasmid containing the TK gene of HVT. The obtained viruses (44%) did not express eGFP, and DNA sequencing of isolated clones revealed that they were completely free of the inserted BAC sequences. Moreover, growth kinetics and plaque morphology of reconstituted viruses were comparable with those of the parental HVT. The results of this study demonstrate that the novel RIBON approach to remove mini-F sequences from the viral genome is simple and effective. PMID:27041357

  17. The BepiColombo Archive Core System (BACS)

    NASA Astrophysics Data System (ADS)

    Macfarlane, A. J.; Osuna, P.; Pérez-López, F.; Vallejo, J. C.; Martinez, S.; Arviset, C.; Casale, M.

    2015-09-01

    BepiColombo is an interdisciplinary ESA mission to explore the planet Mercury in cooperation with JAXA. The mission consists of two separate orbiters: ESA's Mercury Planetary Orbiter (MPO) and JAXA's Mercury Magnetospheric Orbiter (MMO), which are dedicated to the detailed study of the planet and its magnetosphere. The MPO scientific payload comprises 11 instruments covering different scientific disciplines developed by several European teams. The MPO science operations will be prepared by the MPO Science Ground Segment (SGS) located at the European Space Astronomy Centre (ESAC) in Madrid. The BepiColombo Archive Core System (BACS) will be the central archive in which all mission operational data will be stored and is being developed by the Science Archives and Virtual Observatory Team (SAT) also at ESAC. The BACS will act as one of the modular subsystems within the BepiColombo Science Operations Control System (BSCS), (Vallejo 2014; Pérez-López 2014) which is under the responsibility of the SGS, with the purpose of facilitating the information exchange of data and metadata between the other subsystems of the BSCS as well as with the MPO Instrument Teams. This paper gives an overview of the concept and design of the BACS and how it integrates into the science ground segment workflow.

  18. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.

    PubMed

    Dereeper, Alexis; Guyot, Romain; Tranchant-Dubreuil, Christine; Anthony, François; Argout, Xavier; de Bellis, Fabien; Combes, Marie-Christine; Gavory, Frederick; de Kochko, Alexandre; Kudrna, Dave; Leroy, Thierry; Poulain, Julie; Rondeau, Myriam; Song, Xiang; Wing, Rod; Lashermes, Philippe

    2013-10-01

    Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome. PMID:23708951

  19. Time to Detection with BacT/Alert FA Plus Compared to BacT/Alert FA Blood Culture Media.

    PubMed

    Nutman, A; Fisher Even-Tsur, S; Shapiro, G; Braun, T; Schwartz, D; Carmeli, Y

    2016-09-01

    Rapid identification of the causative pathogen in patients with bacteremia allows adjustment of antibiotic therapy and improves patient outcomes. We compared in vitro and real-life time to detection (TTD) of two blood culture media, BacT/Alert FA (FA) and BacT/Alert FA Plus (FA Plus), for the nine most common species of bacterial pathogens recovered from blood samples. Experimental data from simulated cultures was compared with microbiology records of TTD for both culture media with growth of the species of interest in clinical blood cultures. In the experimental conditions, median TTD was 3.8 hours (23.9 %) shorter using FA Plus media. The magnitude of reduction differed between species. Similarly, in real life data, FA Plus had shorter TTD than FA media; however, the difference between culture media was smaller, and median TTD was only 1 hour (8.5 %) less. We found shorter TTD with BacT/Alert FA Plus culture media, both experimentally and in real-life conditions and unrelated to antibiotic neutralization, highlighting the importance of appropriate blood culture media selection. PMID:27272123

  20. Library 2000.

    ERIC Educational Resources Information Center

    Drake, Miriam A.

    In fall 1984, the Georgia Institute of Technology administration and library staff began planning for Library 2000, a project aimed at creating a showcase library to demonstrate the application of the latest information technology in an academic and research environment. The purposes of Library 2000 include: increasing awareness of students,…

  1. Sex Chromosome Evolution in Amniotes: Applications for Bacterial Artificial Chromosome Libraries

    PubMed Central

    Janes, Daniel E.; Valenzuela, Nicole; Ezaz, Tariq; Amemiya, Chris; Edwards, Scott V.

    2011-01-01

    Variability among sex chromosome pairs in amniotes denotes a dynamic history. Since amniotes diverged from a common ancestor, their sex chromosome pairs and, more broadly, sex-determining mechanisms have changed reversibly and frequently. These changes have been studied and characterized through the use of many tools and experimental approaches but perhaps most effectively through applications for bacterial artificial chromosome (BAC) libraries. Individual BAC clones carry 100–200 kb of sequence from one individual of a target species that can be isolated by screening, mapped onto karyotypes, and sequenced. With these techniques, researchers have identified differences and similarities in sex chromosome content and organization across amniotes and have addressed hypotheses regarding the frequency and direction of past changes. Here, we review studies of sex chromosome evolution in amniotes and the ways in which the field of research has been affected by the advent of BAC libraries. PMID:20981143

  2. DNA shuttling between plasmid vectors and a genome vector: systematic conversion and preservation of DNA libraries using the Bacillus subtilis genome (BGM) vector.

    PubMed

    Kaneko, Shinya; Akioka, Manami; Tsuge, Kenji; Itaya, Mitsuhiro

    2005-06-24

    The combined use of the contemporary vector systems, the bacterial artificial chromosome (BAC) vector and the Bacillus subtilis genome (BGM) vector, makes possible the handling of giant-length DNA (above 100 kb). Our newly constructed BGM vector efficiently integrated DNA prepared in the BAC vector. A BAC library comprised of 18 independent clones prepared from mitochondrial DNA (mtDNA) of Arabidopsis thaliana was converted to a parallel BGM library using the new BGM vector. The effectiveness of the combined use of the vector systems was confirmed by the stable recovery of all 18 DNAs as BAC clones from the respective BGM clones. We show that DNA in BGM was stably preserved at room temperature after spore formation of the host B.subtilis. Rapid and stable shuttling between Escherichiacoli and the B. subtilis host, combined with spore-mediated DNA storage, may facilitate the long-term and low-cost preservation and the transportation of DNA resources. PMID:15913652

  3. A FISH approach for mapping the human genome using Bacterial Artificial Chromosomes (BACs)

    SciTech Connect

    Hubert, R.S.; Chen, X.N.; Mitchell, S.

    1994-09-01

    As the Human Genome Project progresses, large insert cloning vectors such as BACs, P1, and P1 Artificial Chromosomes (PACs) will be required to complement the YAC mapping efforts. The value of the BAC vector for physical mapping lies in the stability of the inserts, the lack of chimerism, the length of inserts (up to 300 kb), the ability to obtain large amounts of pure clone DNA and the ease of BAC manipulation. These features helped us design two approaches for generating physical mapping reagents for human genetic studies. The first approach is a whole genome strategy in which randomly selected BACs are mapped, using FISH, to specific chromosomal bands. To date, 700 BACs have been mapped to single chromosome bands at a resolution of 2-5 Mb in addition to BACs mapped to 14 different centromeres. These BACs represent more than 90 Mb of the genome and include >70% of all human chromosome bands at the 350-band level. These data revealed that >97% of the BACs were non-chimeric and have a genomic distribution covering most gaps in the existing YAC map with excellent coverage of gene-rich regions. In the second approach, we used YACs to identify BACs on chromosome 21. A 1.5 Mb contig between D21S339 and D21S220 nears completion within the Down syndrome congenital heart disease (DS-CHD) region. Seventeen BACs ranging in size from 80 kb to 240 kb were ordered using 14 STSs with FISH confirmation. We have also used 40 YACs spanning 21q to identify, on average, >1 BAC/Mb to provide molecular cytogenetic reagents and anchor points for further mapping. The contig generated on chromosome 21 will be helpful in isolating the genes for DS-CHD. The physical mapping reagents generated using the whole genome approach will provide cytogenetic markers and mapped genomic fragments that will facilitate positional cloning efforts and the identification of genes within most chromosomal bands.

  4. Special Libraries

    ERIC Educational Resources Information Center

    Lavendel, Giuliana

    1977-01-01

    Discusses problems involved in maintaining special scientific or engineering libraries, including budget problems, remote storage locations, rental computer retrieval systems, protecting trade secrets, and establishing a magnetic tape library. (MLH)

  5. A non-autonomous insect piggyBac trasposable element is mobile in tobacco

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The piggyBac transposable element, originally isolated from a virus in an insect cell line, is a valuable molecular tool for transgenesis and mutagenesis of invertebrates. For heterologous transgenesis in a variety of mammals, transfer of the piggyBac transposable element from an ectopic plasmid onl...

  6. Protective efficacy of a recombinant BAC clone of Marek's disease virus containing REV-LTR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Insertion of reticuloendotheliosis virus (REV) long-terminal repeat (LTR) into a bacterial artificial chromosome (BAC) clone of a very virulent strain of Marek’s disease (MD) virus (MDV), Md5 (Kim et al, 2011) rendered the resultant recombinant virus termed rMd5 REV-LTR BAC fully attenuated at passa...

  7. 76 FR 44055 - BAC Home Loans Servicing, LP, et al.; Notice of Application and Temporary Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-22

    ... COMMISSION BAC Home Loans Servicing, LP, et al.; Notice of Application and Temporary Order July 18, 2011... Act, with respect to an injunction entered against BAC Home Loans Servicing, LP (``HLS'') on May 31... entered the Injunction against HLS, formerly Countrywide Home Loans Servicing LP, in a matter brought...

  8. Recombineering strategies for developing next generation BAC transgenic tools for optogenetics and beyond

    PubMed Central

    Ting, Jonathan T.; Feng, Guoping

    2014-01-01

    The development and application of diverse BAC transgenic rodent lines has enabled rapid progress for precise molecular targeting of genetically-defined cell types in the mammalian central nervous system. These transgenic tools have played a central role in the optogenetic revolution in neuroscience. Indeed, an overwhelming proportion of studies in this field have made use of BAC transgenic Cre driver lines to achieve targeted expression of optogenetic probes in the brain. In addition, several BAC transgenic mouse lines have been established for direct cell-type specific expression of Channelrhodopsin-2 (ChR2). While the benefits of these new tools largely outweigh any accompanying challenges, many available BAC transgenic lines may suffer from confounds due in part to increased gene dosage of one or more “extra” genes contained within the large BAC DNA sequences. Here we discuss this under-appreciated issue and propose strategies for developing the next generation of BAC transgenic lines that are devoid of extra genes. Furthermore, we provide evidence that these strategies are simple, reproducible, and do not disrupt the intended cell-type specific transgene expression patterns for several distinct BAC clones. These strategies may be widely implemented for improved BAC transgenesis across diverse disciplines. PMID:24772073

  9. Excision of the piggyBac transposable element in maize cells is a precise event

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The piggyBac transposable element (TE) from the moth Trichoplusia ni encodes a ‘cut and paste’ DNA transposase that has been used to transform a number of insects, as well as planaria, mammalian cells, and mice. The wild type and a mutated piggyBac TE excised from a DNA vector in transient assays u...

  10. Use of BAC clones as standardized reagents for Marek’s disease virus research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cloning of the Marek’s disease virus (MDV) genome as an infectious bacterial artificial chromosome (BAC) clone have led to major advances through our ability to study individual gene function by making precise insertions and deletions in the viral genome. We believe that MDV BAC clones will repl...

  11. Library Skills.

    ERIC Educational Resources Information Center

    Paul, Karin; Kuhlthau, Carol C.; Branch, Jennifer L.; Solowan, Diane Galloway; Case, Roland; Abilock, Debbie; Eisenberg, Michael B.; Koechlin, Carol; Zwaan, Sandi; Hughes, Sandra; Low, Ann; Litch, Margaret; Lowry, Cindy; Irvine, Linda; Stimson, Margaret; Schlarb, Irene; Wilson, Janet; Warriner, Emily; Parsons, Les; Luongo-Orlando, Katherine; Hamilton, Donald

    2003-01-01

    Includes 19 articles that address issues related to library skills and Canadian school libraries. Topics include information literacy; inquiry learning; critical thinking and electronic research; collaborative inquiry; information skills and the Big 6 approach to problem solving; student use of online databases; library skills; Internet accuracy;…

  12. Construction of DNA libraries from flow sorted human chromosomes

    SciTech Connect

    Deaven, L.L.; McCormick, M.K.; Grady, D.L.

    1994-09-01

    We have constructed a series of DNA libraries from flow-sorted chromosomes. Small insert, complete digest libraries cloned into the EcoRI insertion site of Charon 21A are available from the American Type Culture Collection, Rockville, MD. Partial digest libraries cloned into cosmid (sCos1) or phage (Charon 40) vectors have been constructed for chromosomes 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, X and Y. Purity estimates by in situ analysis of sorted chromosomes, flow karyotype analysis, and plaque or colony hybridization indicate that most of these libraries are 90-95% pure. Additional cosmid library constructions, 5-10X arrays of libraries into microtiter plates, and high density membrane arrays of libraries are in progress. Recently, we have completed YAC libraries for chromosomes 5, 9, 16, and 21. These libraries are made from complete DNA digests using the rare cutters Clal, SacII, EagI, or NotI/NheI. The average insert size is {similar_to}200 kb, and chimera frequencies are low (1-10%). Libraries have also been constructed using M13 or bluescript vectors (chromosomes 5, 7, 17) to generate STS markers for the selection of chromosome-specific inserts from total genomic AC libraries. Because of the advantages of insert size and stability associated with BAC and PAC cloning systems, we are currently attempting to adapt pBAC108L and pCYPAC1 vectors for use with flow-sorted chromosomal DNA.

  13. Construction of a BAC Library of the Leymus Cinereus X L. Triticoides Hybrid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leymus cinereus and L. triticoides are two wildrye grasses with many contrasting morphological and agronomic traits. The interspecific hybrid Leymus cinereus X L. triticoides and its progenies had been used to develop linkage maps of traits and molecular markers. To generate genomic DNA sequence i...

  14. Metagenomic analysis of Candidatus Liberibacter asiaticus in naturally populated psyllids (Diaphorina citri) using BAC libraries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Candidatus Liberibacter asiaticus (Las) is the most prevalent species of three species of Ca. Liberibacter causing citrus huanglongbing (HLB) in the world. The Las genome sequence published in 2009 was obtained from a single Las-infected psyllid using metagenomic approach. Studies of genetic divers...

  15. A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish

    PubMed Central

    Fuentes, Fernando; Reynolds, Eric; Lewellis, Stephen W.; Venkiteswaran, Gayatri; Knaut, Holger

    2016-01-01

    Transgenesis of large DNA constructs is essential for gene function analysis. Recently, Tol2 transposase-mediated transgenesis has emerged as a powerful tool to insert bacterial artificial chromosome (BAC) DNA constructs into the genome of zebrafish. For efficient transgenesis, the genomic DNA piece in the BAC construct needs to be flanked by Tol2 transposon sites, and the constructs should contain a transgenesis marker for easy identification of transgenic animals. We report a set of plasmids that contain targeting cassettes that allow the insertion of Tol2 sites and different transgenesis markers into BACs. Using BACs containing these targeting cassettes, we show that transgenesis is as efficient as iTol2, that preselecting for expression of the transgenesis marker increases the transgenesis rate, and that BAC transgenics faithfully recapitulate the endogenous gene expression patterns and allow for the estimation of the endogenous gene expression levels. PMID:26818072

  16. A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish.

    PubMed

    Fuentes, Fernando; Reynolds, Eric; Lewellis, Stephen W; Venkiteswaran, Gayatri; Knaut, Holger

    2016-01-01

    Transgenesis of large DNA constructs is essential for gene function analysis. Recently, Tol2 transposase-mediated transgenesis has emerged as a powerful tool to insert bacterial artificial chromosome (BAC) DNA constructs into the genome of zebrafish. For efficient transgenesis, the genomic DNA piece in the BAC construct needs to be flanked by Tol2 transposon sites, and the constructs should contain a transgenesis marker for easy identification of transgenic animals. We report a set of plasmids that contain targeting cassettes that allow the insertion of Tol2 sites and different transgenesis markers into BACs. Using BACs containing these targeting cassettes, we show that transgenesis is as efficient as iTol2, that preselecting for expression of the transgenesis marker increases the transgenesis rate, and that BAC transgenics faithfully recapitulate the endogenous gene expression patterns and allow for the estimation of the endogenous gene expression levels. PMID:26818072

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

    SciTech Connect

    Lim, C.S.; Xu, R.X.; Wang, M.

    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).

  18. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

    PubMed Central

    Bartoš, Jan; Paux, Etienne; Kofler, Robert; Havránková, Miroslava; Kopecký, David; Suchánková, Pavla; Šafář, Jan; Šimková, Hana; Town, Christopher D; Lelley, Tamas; Feuillet, Catherine; Doležel, Jaroslav

    2008-01-01

    Background Rye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding. Results Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers. Conclusion This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1. PMID:18803819

  19. Superconductivity in the Graphite Intercalation Compound BaC 6

    NASA Astrophysics Data System (ADS)

    Heguri, Satoshi; Kawade, Naoya; Fujisawa, Takumi; Yamaguchi, Akira; Sumiyama, Akihiko; Tanigaki, Katsumi; Kobayashi, Mototada

    2015-06-01

    Among many two-dimensional (2D) high TC superconductors, graphite intercalation compounds (GICs) are the most famous intercalation family, which are classified as typical electron-phonon mediated superconductors. We show unambiguous experimental facts that BaC 6 , the superconductivity of which has been missing for many years so far among various alkaline earth metal (Ca, Sr, and Ba) intercalted GICs, exhibits superconductivity at TC=65 mK . By adding this finding as the additional experimental point, a complete figure displaying the relationship between TC and interlayer distance (d ) for GICs is now provided, and their possible superconducting mechanisms raised so far are revisited. The present study settles a long-running debate between theories and experiments on the superconductivity in the first stage GICs.

  20. Isolation of rare recombinants without using selectable markers for one-step seamless BAC mutagenesis

    PubMed Central

    Lyozin, George T.; Kosaka, Yasuhiro; Demarest, Bradley L.; Yost, H. Joseph; Kuehn, Michael R.; Brunelli, Luca

    2014-01-01

    Current laboratory methods to isolate rare (1:10,000 to 1:100,000) bacterial artificial chromosome (BAC) recombinants require selectable markers. Seamless BAC mutagenesis needs two steps: isolation of rare recombinants using selectable markers, followed by marker removal through counterselection. Here we illustrate founder principle-driven enrichment (FPE), a simple method developed to rapidly isolate rare recombinants without using selectable markers, allowing one-step seamless BAC mutagenesis. As proof-of-principle, we isolated 1:100,000 seamless fluorescent protein-modified Nodal BACs via FPE and confirmed BAC functionality by generating fluorescent reporter mice. We also isolated small indel P1-phage derived artificial chromosome (PAC) and BAC recombinants. Statistical analysis revealed that 1:100,000 recombinants can be isolated running <40 PCRs and we developed a web-based calculator to optimize FPE. By eliminating the need for selection-counterselection, this work highlights a straightforward and low-cost approach to BAC mutagenesis, providing a tool for seamless recombineering pipelines in functional genomics. PMID:25028895

  1. Precise marker excision system using an animal-derived piggyBac transposon in plants.

    PubMed

    Nishizawa-Yokoi, Ayako; Endo, Masaki; Osakabe, Keishi; Saika, Hiroaki; Toki, Seiichi

    2014-02-01

    Accurate and effective positive marker excision is indispensable for the introduction of desired mutations into the plant genome via gene targeting (GT) using a positive/negative counter selection system. In mammals, the moth-derived piggyBac transposon system has been exploited successfully to eliminate a selectable marker from a GT locus without leaving a footprint. Here, we present evidence that the piggyBac transposon also functions in plant cells. To demonstrate the use of the piggyBac transposon for effective marker excision in plants, we designed a transposition assay system that allows the piggyBac transposition to be visualized as emerald luciferase (Eluc) luminescence in rice cells. The Eluc signal derived from piggyBac excision was observed in hyperactive piggyBac transposase-expressing rice calli. Polymerase chain reaction, Southern blot analyses and sequencing revealed the efficient and precise transposition of piggyBac in these calli. Furthermore, we have demonstrated the excision of a selection marker from a reporter locus in T0 plants without concomitant re-integration of the transposon and at a high frequency (44.0% of excision events), even in the absence of negative selection. PMID:24164672

  2. Precise marker excision system using an animal-derived piggyBac transposon in plants

    PubMed Central

    Nishizawa-Yokoi, Ayako; Endo, Masaki; Osakabe, Keishi; Saika, Hiroaki; Toki, Seiichi

    2014-01-01

    Accurate and effective positive marker excision is indispensable for the introduction of desired mutations into the plant genome via gene targeting (GT) using a positive/negative counter selection system. In mammals, the moth-derived piggyBac transposon system has been exploited successfully to eliminate a selectable marker from a GT locus without leaving a footprint. Here, we present evidence that the piggyBac transposon also functions in plant cells. To demonstrate the use of the piggyBac transposon for effective marker excision in plants, we designed a transposition assay system that allows the piggyBac transposition to be visualized as emerald luciferase (Eluc) luminescence in rice cells. The Eluc signal derived from piggyBac excision was observed in hyperactive piggyBac transposase-expressing rice calli. Polymerase chain reaction, Southern blot analyses and sequencing revealed the efficient and precise transposition of piggyBac in these calli. Furthermore, we have demonstrated the excision of a selection marker from a reporter locus in T0 plants without concomitant re-integration of the transposon and at a high frequency (44.0% of excision events), even in the absence of negative selection. PMID:24164672

  3. Post-integration stability of piggyBac in Aedes aegypti.

    PubMed

    Sethuraman, Nagaraja; Fraser, Malcolm J; Eggleston, Paul; O'Brochta, David A

    2007-09-01

    The post-integration activity of piggyBac transposable element gene vectors in Aedes aegypti mosquitoes was tested under a variety of conditions. The embryos from five independent transgenic lines of Ae. aegypti, each with a single integrated non-autonomous piggyBac transposable element gene vector, were injected with plasmids containing the piggyBac transposase open-reading frame under the regulatory control of the Drosophila melanogaster hsp70 promoter. No evidence for somatic remobilization was detected in the subsequent adults whereas somatic remobilization was readily detected when similar lines of transgenic D. melanogaster were injected with the same piggyBac transposase-expressing plasmid. Ae. aegypti heterozygotes of piggyBac reporter-containing transgenes and piggyBac transposase-expressing transgenes showed no evidence of somatic and germ-line remobilization based on phenotypic and molecular detection methods. The post-integration mobility properties of piggyBac in Ae. aegypti enhance the utility of this gene vector for certain applications, particularly those where any level of vector remobilization is unacceptable. PMID:17681233

  4. Libraries program

    USGS Publications Warehouse

    2011-01-01

    The U.S. Congress authorized a library for the U.S. Geological Survey (USGS) in 1879. The library was formally established in 1882 with the naming of the first librarian and began with a staff of three and a collection of 1,400 books. Today, the USGS Libraries Program is one of the world's largest Earth and natural science repositories and a resource of national significance used by researchers and the public worldwide.

  5. Conversion of BAC clones into binary BAC (BIBAC) vectors and their delivery into basidiomycete fungal cells using Agrobacterium tumefaciens.

    PubMed

    Ali, Shawkat; Bakkeren, Guus

    2015-01-01

    The genetic transformation of certain organisms, required for gene function analysis or complementation, is often not very efficient, especially when dealing with large gene constructs or genomic fragments. We have adapted the natural DNA transfer mechanism from the soil pathogenic bacterium Agrobacterium tumefaciens, to deliver intact large DNA constructs to basidiomycete fungi of the genus Ustilago where they stably integrated into their genome. To this end, Bacterial Artificial Chromosome (BAC) clones containing large fungal genomic DNA fragments were converted via a Lambda phage-based recombineering step to Agrobacterium transfer-competent binary vectors (BIBACs) with a Ustilago-specific selection marker. The fungal genomic DNA fragment was subsequently successfully delivered as T-DNA through Agrobacterium-mediated transformation into Ustilago species where an intact copy stably integrated into the genome. By modifying the recombineering vector, this method can theoretically be adapted for many different fungi. PMID:25239747

  6. BacPP: a web-based tool for Gram-negative bacterial promoter prediction.

    PubMed

    de Avila E Silva, S; Notari, D L; Neis, F A; Ribeiro, H G; Echeverrigaray, S

    2016-01-01

    Bacterial Promoter Prediction (BacPP) is a tool used to predict given sequences as promoters of Gram-negative bacteria according to the σ factor that recognizes it. The first version of BacPP was implemented in Python language in a desktop version without a friendly interface. For this reason, a web version of BacPP is now available with the purpose of improving its usability and availability. The present paper describes the implementation of the web version of this tool, focusing on its software architecture and user functionalities. The software is available at www.bacpp.bioinfoucs.com/home. PMID:27173187

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

    ERIC Educational Resources Information Center

    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. Privatizing Libraries

    ERIC Educational Resources Information Center

    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…

  9. Library Advocacy

    ERIC Educational Resources Information Center

    Plunkett, Kate

    2010-01-01

    This paper is about the issue of advocacy. Standing at the vanguard of literacy, library media specialists have a unique role. However, it is time for media specialists to advocate their services in a proactive way. If library media specialists cannot, both individually and collectively, put advocacy at the forefront, then students will suffer the…

  10. Macintoshed Libraries.

    ERIC Educational Resources Information Center

    Valauskas, Edward J., Ed.; John, Nancy R., Ed.

    Contributed by librarians from public, academic, school, and special libraries, the 17 essays in this collection describe ways in which the Apple Macintosh is used in their libraries: (1) "Workstations and the Apple Macintosh" (Edward J. Valauskas); (2) "The Macintosh Experience at Chesapeake College" (Liz Cooper); (3) "ANSEL Character Set for the…

  11. Library Lighting.

    ERIC Educational Resources Information Center

    Metcalf, Keyes D.

    Chapter I provides a background and explains pertinent library lighting problems such as quality, function, aesthetics, intensity, and costs. Emphasis is on the quality and function of lighting for library users. Chapter II deals with the comments and answers to questions by persons who have a special interest and competence in the field of…

  12. Library Research.

    ERIC Educational Resources Information Center

    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…

  13. Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences

    PubMed Central

    Dougherty, William M.; Martínez-García, Pedro J.; Koriabine, Maxim; Holtz-Morris, Ann; deJong, Pieter; Crepeau, Marc; Langley, Charles H.; Puiu, Daniela; Salzberg, Steven L.; Neale, David B.; Stevens, Kristian A.

    2013-01-01

    Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution. PMID:24023741

  14. Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

    PubMed

    Wegrzyn, Jill L; Lin, Brian Y; Zieve, Jacob J; Dougherty, William M; Martínez-García, Pedro J; Koriabine, Maxim; Holtz-Morris, Ann; deJong, Pieter; Crepeau, Marc; Langley, Charles H; Puiu, Daniela; Salzberg, Steven L; Neale, David B; Stevens, Kristian A

    2013-01-01

    Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution. PMID:24023741

  15. Construction and characterization of an eightfold redundant dog genomic bacterial artificial chromosome library.

    PubMed

    Li, R; Mignot, E; Faraco, J; Kadotani, H; Cantanese, J; Zhao, B; Lin, X; Hinton, L; Ostrander, E A; Patterson, D F; de Jong, P J

    1999-05-15

    A large insert canine genomic bacterial artificial chromosome (BAC) library was built from a Doberman pinscher. Approximately 166,000 clones were gridded on nine high-density hybridization filters. Insert analysis of randomly selected clones indicated a mean insert size of 155 kb and predicted 8.1 coverage of the canine genome. Two percent of the clones were nonrecombinant. Chromosomal fluorescence in situ hybridization studies of 60 BAC clones indicated no chimerism. The library was hybridized with dog PCR products representing eight genes (ADA, TNFA, GCA, MYB, HOXA, GUSB, THY1, and TOP1). The resulting positive clones were characterized and shown to be compatible with an eightfold redundant library. PMID:10331940

  16. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

    PubMed Central

    Wang, Wenming; Tanurdzic, Milos; Luo, Meizhong; Sisneros, Nicholas; Kim, Hye Ran; Weng, Jing-Ke; Kudrna, Dave; Mueller, Christopher; Arumuganathan, K; Carlson, John; Chapple, Clint; de Pamphilis, Claude; Mandoli, Dina; Tomkins, Jeff; Wing, Rod A; Banks, Jo Ann

    2005-01-01

    Background The lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants. Results Here we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones; the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes. Conclusion The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution. PMID:15955246

  17. 23 CFR 1225.4 - Adoption of 0.08 BAC per se law.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Adoption of 0.08 BAC per se law. 1225.4 Section 1225.4... TRANSPORTATION GUIDELINES OPERATION OF MOTOR VEHICLES BY INTOXICATED PERSONS § 1225.4 Adoption of 0.08 BAC per se... is enforcing a law that provides that any person with a blood or breath alcohol concentration...

  18. Generation of knockout alleles by RFLP based BAC targeting of polymorphic embryonic stem cells.

    PubMed

    Barakat, Tahsin Stefan; Gribnau, Joost

    2015-01-01

    The isolation of germ line competent mouse Embryonic Stem (ES) cells and the ability to modify the genome by homologous recombination has revolutionized life science research. Since its initial discovery, several approaches have been introduced to increase the efficiency of homologous recombination, including the use of isogenic DNA for the generation of targeting constructs, and the use of Bacterial Artificial Chromosomes (BACs). BACs have the advantage of combining long stretches of homologous DNA, thereby increasing targeting efficiencies, with the possibilities delivered by BAC recombineering approaches, which provide the researcher with almost unlimited possibilities to efficiently edit the genome in a controlled fashion. Despite these advantages of BAC targeting approaches, a widespread use has been hampered, mainly because of the difficulties in identifying BAC-targeted knockout alleles by conventional methods like Southern Blotting. Recently, we introduced a novel BAC targeting strategy, in which Restriction Fragment Length Polymorphisms (RFLPs) are targeted in polymorphic mouse ES cells, enabling an efficient and easy PCR-based readout to identify properly targeted alleles. Here we provide a detailed protocol for the generation of targeting constructs, targeting of ES cells, and convenient PCR-based analysis of targeted clones, which enable the user to generate knockout ES cells of almost every gene in the mouse genome within a 2-month period. PMID:25239745

  19. Strain-Specific Regulation of Striatal Phenotype in Drd2-eGFP BAC Transgenic Mice

    PubMed Central

    Chan, C. Savio; Peterson, Jayms D.; Gertler, Tracy S.; Glajch, Kelly E.; Quintana, Ruth E.; Cui, Qiaoling; Sebel, Luke E.; Plotkin, Joshua L.; Shen, Weixing; Heiman, Myriam; Heintz, Nathaniel; Greengard, Paul; Surmeier, D. James

    2012-01-01

    Mice carrying bacterial artificial chromosome (BAC) transgenes have become important tools for neuroscientists, providing a powerful means of dissecting complex neural circuits in the brain. Recently, it was reported that one popular line of these mice – mice possessing a BAC transgene with a D2 dopamine receptor (Drd2) promoter construct coupled to an enhanced green fluorescent protein (eGFP) reporter – had abnormal striatal gene expression, physiology and motor behavior. Unlike most of the work using BAC mice, this interesting study relied upon mice backcrossed on the outbred Swiss Webster strain that were homozygous for the Drd2-eGFP BAC transgene.The experiments reported here were conducted to determine whether mouse strain or zygosity was a factor in the reported abnormalities. As reported, SW mice were very sensitive to transgene expression. However, in more commonly used inbred strains of mice (C57BL/6, FVB/N) that were hemizygous for the transgene, the Drd2-eGFP BAC transgene did not alter striatal gene expression, physiology or motor behavior. Thus, the use of inbred strains of mice which are hemizygous for the Drd2 BAC transgene provide a reliable tool for studying basal ganglia function. PMID:22764222

  20. Hybrid nonviral/viral vector systems for improved piggyBac DNA transposon in vivo delivery.

    PubMed

    Cooney, Ashley L; Singh, Brajesh K; Sinn, Patrick L

    2015-04-01

    The DNA transposon piggyBac is a potential therapeutic agent for multiple genetic diseases such as cystic fibrosis (CF). Recombinant piggyBac transposon and transposase are typically codelivered by plasmid transfection; however, plasmid delivery is inefficient in somatic cells in vivo and is a barrier to the therapeutic application of transposon-based vector systems. Here, we investigate the potential for hybrid piggyBac/viral vectors to transduce cells and support transposase-mediated genomic integration of the transposon. We tested both adenovirus (Ad) and adeno-associated virus (AAV) as transposon delivery vehicles. An Ad vector expressing hyperactive insect piggyBac transposase (iPB7) was codelivered. We show transposase-dependent transposition activity and mapped integrations in mammalian cells in vitro and in vivo from each viral vector platform. We also demonstrate efficient and persistent transgene expression following nasal delivery of piggyBac/viral vectors to mice. Furthermore, using piggyBac/Ad expressing Cystic Fibrosis transmembrane Conductance Regulator (CFTR), we show persistent correction of chloride current in well-differentiated primary cultures of human airway epithelial cells derived from CF patients. Combining the emerging technologies of DNA transposon-based vectors with well-studied adenoviral and AAV delivery provides new tools for in vivo gene transfer and presents an exciting opportunity to increase the delivery efficiency for therapeutic genes such as CFTR. PMID:25557623

  1. Measurement Properties of the Low Back Activity Confidence Scale (LoBACS).

    PubMed

    Davenport, Todd E; Cleland, Joshua A; Yamada, Kimiko A; Kulig, Kornelia

    2016-06-01

    The purpose of this study was to determine the measurement properties of the Low Back Activity Confidence Scale (LoBACS) in individuals with post-acute low back pain (LBP) receiving nonsurgical intervention, including construct validity, factorial validity, and internal consistency reliability. Data were analyzed from an existing randomized clinical trial involving 112 patients with LBP. Evidence for convergent validity was observed through significant correlations between LoBACS subscale scores and other function, pain, and psychobehavioral measures. LoBACS subscales accounted for 36% of the unique variance in dependent variable measurements, suggesting a satisfactory level of statistical divergence between the LoBACS and other psychobehavioral measurements in this study. Cronbach's α ranged from .88 to .92 for LoBACS subscales, and item-total correlations exceeded .6, indicating high internal consistency reliability. Principal axis factoring confirmed the hypothesized three-subscale structure by correctly classifying 14 of the 15 items. These findings indicate the LoBACS is valid and internally consistent to measure domain-specific self-efficacy beliefs. PMID:24686745

  2. A Low-Copy-Number Plasmid for Retrieval of Toxic Genes from BACs and Generation of Conditional Targeting Constructs

    PubMed Central

    Na, Giyoun; Wolfe, Andrew; Ko, CheMyong; Youn, Hyesook; Lee, Young-Min; Byun, Sung June; Jeon, Iksoo

    2016-01-01

    Bacterial Artificial Chromosome (BAC) clones are widely used for retrieving genomic DNA sequences for gene targeting. In this study, low-copy-number plasmids pBAC-FB, pBAC-FC, and pBAC-DE, which carry the F plasmid replicon, were generated from pBACe3.6. pBAC-FB was successfully used to retrieve a sequence of a BAC that was resistant to retrieval by a high-copy-number plasmid via λ Red-mediated recombineering (gap-repair cloning). This plasmid was also used to retrieve two other genes from BAC, indicating its general usability retrieving genes from BAC. The retrieved genes were manipulated in generating targeting vectors for gene knockouts by recombineering. The functionality of the targeting vector was further validated in a targeting experiment with C57BL/6 embryonic stem cells. The low-copy-number plasmid pBAC-FB is a plasmid of choice to retrieve toxic DNA sequences from BACs and to manipulate them to generate gene-targeting constructs by recombineering. PMID:22945876

  3. A high-density physical map of Sinorhizobium meliloti 1021 chromosome derived from bacterial artificial chromosome library

    PubMed Central

    Capela, Delphine; Barloy-Hubler, Frédérique; Gatius, Marie-Thérèse; Gouzy, Jérôme; Galibert, Francis

    1999-01-01

    As part of the European Sinorhizobium meliloti (strain 1021) chromosome sequencing project, four genomic bacterial artificial chromosome (BAC) libraries have been constructed, one of which was mainly used for chromosome mapping. This library consists of 1,824 clones with an average insert size of 80 kilobases and represents approximately 20-fold total genome coverage [6.8 megabases (Mbs)]. PCR screening of 384 BAC clones with 447 chromosomal markers (PCR primer pairs), consisting of 73 markers representing 118 genes (40 individual genes and 78 genes clustered in 23 operons), two markers from the rrn operon (three loci), four markers from insertion sequences (≈16 loci) and 368 sequence-tagged sites allowed the identification of 252 chromosomal BAC clones and the construction of a high-density physical map of the whole 3.7-Mb chromosome of S. meliloti. An average of 5.5 overlapping and colinear BAC clones per marker, correlated with a low rate of deleted or rearranged clones (0.8%) indicate a solid BAC contigation and a correct mapping. Systematic blastx analysis of sequence-tagged site marker sequences allowed prediction of a biological function for a number of putative ORFs. Results are available at http://www-recomgen.univ-rennes1.fr/meliloti. This map, whose resolution averages one marker every 9 kilobases, should provide a valuable tool for further sequencing, functional analysis, and positional cloning. PMID:10430947

  4. Callpath Library

    SciTech Connect

    Gamblin, T.

    2013-11-09

    The "Callpath Library" is a software abstraction layer over a number of stack tracing utilities. It allows tool develoopers to conveniently represent and mNipulate call paths gathered fro U. Wisconsin's Stackwalker API and GNU Backtrace.

  5. Academic Libraries

    ERIC Educational Resources Information Center

    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)

  6. Digital Libraries.

    ERIC Educational Resources Information Center

    Fox, Edward A.; Urs, Shalini R.

    2002-01-01

    Provides an overview of digital libraries research, practice, and literature. Highlights include new technologies; redefining roles; historical background; trends; creating digital content, including conversion; metadata; organizing digital resources; services; access; information retrieval; searching; natural language processing; visualization;…

  7. Ataxin-2 regulates RGS8 translation in a new BAC-SCA2 transgenic mouse model.

    PubMed

    Dansithong, Warunee; Paul, Sharan; Figueroa, Karla P; Rinehart, Marc D; Wiest, Shaina; Pflieger, Lance T; Scoles, Daniel R; Pulst, Stefan M

    2015-04-01

    Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant disorder with progressive degeneration of cerebellar Purkinje cells (PCs) and other neurons caused by expansion of a glutamine (Q) tract in the ATXN2 protein. We generated BAC transgenic lines in which the full-length human ATXN2 gene was transcribed using its endogenous regulatory machinery. Mice with the ATXN2 BAC transgene with an expanded CAG repeat (BAC-Q72) developed a progressive cellular and motor phenotype, whereas BAC mice expressing wild-type human ATXN2 (BAC-Q22) were indistinguishable from control mice. Expression analysis of laser-capture microdissected (LCM) fractions and regional expression confirmed that the BAC transgene was expressed in PCs and in other neuronal groups such as granule cells (GCs) and neurons in deep cerebellar nuclei as well as in spinal cord. Transcriptome analysis by deep RNA-sequencing revealed that BAC-Q72 mice had progressive changes in steady-state levels of specific mRNAs including Rgs8, one of the earliest down-regulated transcripts in the Pcp2-ATXN2[Q127] mouse line. Consistent with LCM analysis, transcriptome changes analyzed by deep RNA-sequencing were not restricted to PCs, but were also seen in transcripts enriched in GCs such as Neurod1. BAC-Q72, but not BAC-Q22 mice had reduced Rgs8 mRNA levels and even more severely reduced steady-state protein levels. Using RNA immunoprecipitation we showed that ATXN2 interacted selectively with RGS8 mRNA. This interaction was impaired when ATXN2 harbored an expanded polyglutamine. Mutant ATXN2 also reduced RGS8 expression in an in vitro coupled translation assay when compared with equal expression of wild-type ATXN2-Q22. Reduced abundance of Rgs8 in Pcp2-ATXN2[Q127] and BAC-Q72 mice supports our observations of a hyper-excitable mGluR1-ITPR1 signaling axis in SCA2, as RGS proteins are linked to attenuating mGluR1 signaling. PMID:25902068

  8. Standards for British Libraries.

    ERIC Educational Resources Information Center

    Vaughan, Anthony

    1982-01-01

    Reviews developments in British library standards since 1971, highlighting types of standards, public libraries, academic libraries (university, polytechnic, college), school libraries, and special libraries (hospital and health sciences, prison, subject specializations). Thirty-nine references are cited. (EJS)

  9. Germ-line transformation of the Queensland fruit fly, Bactrocera tryoni, using a piggyBac vector in the presence of endogenous piggyBac elements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report the stable genetic transformation of the Queensland fruit fly Bactrocera tryoni using a piggyBac vector marked with either the fluorescent protein DsRed or EGFP.A transformation frequency of 5–10% was obtained.Inheritance of the transgenes has remained stable over eight generations despite...

  10. Survey of 42,000 Gossypium hirsutum cv. Maxxa BAC-End Sequences and Frequency, Type, and Annotation of BAC-derived SSRs.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The quest for more molecular markers is a major initiative in cotton, which lags behind crops such as soybean, maize, and rice in this type of research. In an effort to increase the number of microsatellite markers in Gossypium, BAC-end sequences from a publicly available Gossypium hirsutum cv. Maxx...

  11. Use of Baculovirus BacMam Vectors for Expression of ABC Drug Transporters in Mammalian Cells

    PubMed Central

    Shukla, Suneet; Schwartz, Candice; Kapoor, Khyati; Kouanda, Abdul

    2012-01-01

    ATP-binding cassette (ABC) drug transporters ABCB1 [P-glycoprotein (Pgp)] and ABCG2 are expressed in many tissues including those of the intestines, the liver, the kidney and the brain and are known to influence the pharmacokinetics and toxicity of therapeutic drugs. In vitro studies involving their functional characteristics provide important information that allows improvements in drug delivery or drug design. In this study, we report use of the BacMam (baculovirus-based expression in mammalian cells) expression system to express and characterize the function of Pgp and ABCG2 in mammalian cell lines. BacMam-Pgp and BacMam-ABCG2 baculovirus-transduced cell lines showed similar cell surface expression (as detected by monoclonal antibodies with an external epitope) and transport function of these transporters compared to drug-resistant cell lines that overexpress the two transporters. Transient expression of Pgp was maintained in HeLa cells for up to 72 h after transduction (48 h after removal of the BacMam virus). These BacMam-baculovirus-transduced mammalian cells expressing Pgp or ABCG2 were used for assessing the functional activity of these transporters. Crude membranes isolated from these cells were further used to study the activity of these transporters by biochemical techniques such as photo-cross-linking with transport substrate and adenosine triphosphatase assays. In addition, we show that the BacMam expression system can be exploited to coexpress both Pgp and ABCG2 in mammalian cells to determine their contribution to the transport of a common anticancer drug substrate. Collectively, these data demonstrate that the BacMam-baculovirus-based expression system can be used to simultaneously study the transport function and biochemical properties of ABC transporters. PMID:22041108

  12. Use of baculovirus BacMam vectors for expression of ABC drug transporters in mammalian cells.

    PubMed

    Shukla, Suneet; Schwartz, Candice; Kapoor, Khyati; Kouanda, Abdul; Ambudkar, Suresh V

    2012-02-01

    ATP-binding cassette (ABC) drug transporters ABCB1 [P-glycoprotein (Pgp)] and ABCG2 are expressed in many tissues including those of the intestines, the liver, the kidney and the brain and are known to influence the pharmacokinetics and toxicity of therapeutic drugs. In vitro studies involving their functional characteristics provide important information that allows improvements in drug delivery or drug design. In this study, we report use of the BacMam (baculovirus-based expression in mammalian cells) expression system to express and characterize the function of Pgp and ABCG2 in mammalian cell lines. BacMam-Pgp and BacMam-ABCG2 baculovirus-transduced cell lines showed similar cell surface expression (as detected by monoclonal antibodies with an external epitope) and transport function of these transporters compared to drug-resistant cell lines that overexpress the two transporters. Transient expression of Pgp was maintained in HeLa cells for up to 72 h after transduction (48 h after removal of the BacMam virus). These BacMam-baculovirus-transduced mammalian cells expressing Pgp or ABCG2 were used for assessing the functional activity of these transporters. Crude membranes isolated from these cells were further used to study the activity of these transporters by biochemical techniques such as photo-cross-linking with transport substrate and adenosine triphosphatase assays. In addition, we show that the BacMam expression system can be exploited to coexpress both Pgp and ABCG2 in mammalian cells to determine their contribution to the transport of a common anticancer drug substrate. Collectively, these data demonstrate that the BacMam-baculovirus-based expression system can be used to simultaneously study the transport function and biochemical properties of ABC transporters. PMID:22041108

  13. Efficient production of transgenic chickens based on piggyBac.

    PubMed

    Liu, Xiaojuan; Li, Ning; Hu, Xiaoxiang; Zhang, Ran; Li, Qingyuan; Cao, Dainan; Liu, Tongxin; Zhang, Yaqiong; Liu, Xiaofang

    2013-04-01

    Transgenic techniques in chickens have been developed much more slowly than in mammals due to chickens' unique reproduction mechanism. Retroviral methods have been the most successful. piggyBac (PB) is a transposon that has a 13 bp perfect terminal invert repeat sequence. PB can be inserted into TTAA sites and can also be precisely excised in mammals. Therefore, we have selected PB as a candidate to establish a new method to produce transgenic chickens. We constructed three donor vectors (ZGl-neo, ZGm-neo and ZGs-neo) expressing a GFP marker-gene and a neomycin resistant gene based on PB. We co-transfected each donor vector with a helper vector (CAG-PBase). We found that ZGl-neo was the most efficient PB vector. This vector could insert into TTAA sites in DF-1 cells. PB vectors were microinjected into sub-germinal cavity of newly laid eggs, and electroporation was then performed with a 20-V pulse for 5 cycles of 50 ms on and 100 ms off. GFP was expressed in different tissues of the embryos, including the gonads. Twenty-two chickens hatched after microinjection with compounds ZGl-neo and CAG-PBase (3:1). When we screened the blood DNA, 73 % (16/22) of the individuals were positive. Thirteen of the chickens grew to adulthood, 11 of which were males. 40 % (4/10) of the individuals were semen positive, and their copy numbers ranged from 0.05 to 0.21 (0.11, 0.21, 0.05, 0.06). No G1 offspring containing the integrated transposon were produced. We conclude that the PB transposon system is a novel useful tool for the efficient production of transgenic chickens. PMID:22918673

  14. Stereochemical Outcome at Four Stereogenic Centers During Conversion of Prephenate to Tetrahydrotyrosine by BacABGF in the Bacilysin Pathway†

    PubMed Central

    Parker, Jared B.; Walsh, Christopher T.

    2012-01-01

    The first four enzymes of the bacilysin antibiotic pathway, BacABGF, convert prephenate to a tetrahydrotyrosine (H4Tyr) diastereomer on the way to the anticapsin warhead of the dipeptide antibiotic. BacB takes the BacA product endocyclic-Δ4,Δ8-7R-dihydrohydroxyphenylpyruvate (en-H2HPP) and generates a mixture of 3E- and 3Z-olefins of the exocyclic-Δ3,Δ5-dihydrohydroxyphenylpyruvate (ex-H2HPP). The NADH-utilizing BacG then catalyzes a conjugate reduction, adding a pro-S hydride equivalent to C4 to yield tetrahydrohydroxyphenylpyruvate (H4HPP), a transamination away (via BacF) from 2S-H4Tyr. Incubations of the pathway enzymes in D2O yield deuterium incorporation at C8 from BacA and then C9 from BacB action. By 1H-NMR analysis on samples of H4Tyr, the stereochemistry at C4, C8 and C9 can be assigned. BacG (followed by BacF) converts 3E-ex-H2HPP to 2S, 4R, 7R-H4Tyr. The 3Z isomer is instead reduced and transaminated to the opposite diastereomer at C4: 2S, 4S, 7R-H4Tyr. Given that bacilysin has the 2S, 4S stereochemistry in its anticapsin moiety, it is likely that the 2S, 4S-H4Tyr is the diastereomer “on pathway”. NMR determination of the stereochemistry of the CHD samples at C8 and C9 allow assignment of all stereogenic centers (except C3) in this unusual tetrahydro- aromatic amino acid building block, giving insights and constraints on the BacA, BacB, and BacG mechanisms. PMID:22765234

  15. Computational analysis of ordering in non-liquid crystalline versus liquid crystalline materials with special reference to nBAC

    SciTech Connect

    Lakshmi Praveen, P.; Veera Bhadra Reddy, K.; Ajeetha, N.; Ojha, D. P.

    2009-12-15

    A computational analysis of ordering in non-liquid crystalline p-n-alkyl benzoic acid, having 1 (1BAC), 2 (2BAC) and 3(3BAC) carbon atoms in the alkyl chain has been carried out with respect to translatory and orientational motions, but detailed results are reported only for 3BAC. The evaluation of net atomic charges and dipole moments at each atomic center has been carried out using complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrodinger perturbation theory along with the multicentered-multipole expansion method has been employed to evaluate long-range interactions, while a '6-exp' potential function has been assumed for short-range interactions. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible arrangements of a molecular pair have been considered. A comparative picture of molecular parameters, such as total energy, binding energy, and total dipole moment of 3BAC with higher homologous series liquid crystalline compounds having 4(4BAC), 5(5BAC), and 6(6BAC) alkyl chain carbon atoms, has been given. It is found that, if a suitable functional group is attached to 3BAC, so that the length to breadth ratio is increased, the molecule will show a change in the long-range order, the phase transition temperature and other liquid crystalline properties.

  16. PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice.

    PubMed

    Rad, Roland; Rad, Lena; Wang, Wei; Cadinanos, Juan; Vassiliou, George; Rice, Stephen; Campos, Lia S; Yusa, Kosuke; Banerjee, Ruby; Li, Meng Amy; de la Rosa, Jorge; Strong, Alexander; Lu, Dong; Ellis, Peter; Conte, Nathalie; Yang, Fang Tang; Liu, Pentao; Bradley, Allan

    2010-11-19

    Transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes. Here, we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice. PiggyBac transposition in genetically engineered transposon-transposase mice induced cancers whose type (hematopoietic versus solid) and latency were dependent on the regulatory elements introduced into transposons. Analysis of 63 hematopoietic tumors revealed that PiggyBac is capable of genome-wide mutagenesis. The PiggyBac screen uncovered many cancer genes not identified in previous retroviral or Sleeping Beauty transposon screens, including Spic, which encodes a PU.1-related transcription factor, and Hdac7, a histone deacetylase gene. PiggyBac and Sleeping Beauty have different integration preferences. To maximize the utility of the tool, we engineered 21 mouse lines to be compatible with both transposon systems in constitutive, tissue- or temporal-specific mutagenesis. Mice with different transposon types, copy numbers, and chromosomal locations support wide applicability. PMID:20947725

  17. Insertional Mutagenesis by a Hybrid PiggyBac and Sleeping Beauty Transposon in the Rat

    PubMed Central

    Furushima, Kenryo; Jang, Chuan-Wei; Chen, Diane W.; Xiao, Ningna; Overbeek, Paul A.; Behringer, Richard R.

    2012-01-01

    A hybrid piggyBac/Sleeping Beauty transposon-based insertional mutagenesis system that can be mobilized by simple breeding was established in the rat. These transposons were engineered to include gene trap sequences and a tyrosinase (Tyr) pigmentation reporter to rescue the albinism of the genetic background used in the mutagenesis strategy. Single-copy transposon insertions were transposed into the rat genome by co-injection of plasmids carrying the transposon and RNA encoding piggyBac transposase into zygotes. The levels of transgenic Tyr expression were influenced by chromosomal context, leading to transgenic rats with different pigmentation that enabled visual genotyping. Transgenic rats designed to ubiquitously express either piggyBac or Sleeping Beauty transposase were generated by standard zygote injection also on an albino background. Bigenic rats carrying single-copy transposons at known loci and transposase transgenes exhibited coat color mosaicism, indicating somatic transposition. PiggyBac or Sleeping Beauty transposase bigenic rats bred with wild-type albino rats yielded offspring with pigmentation distinct from the initial transposon insertions as a consequence of germline transposition to new loci. The germline transposition frequency for Sleeping Beauty and piggyBac was ∼10% or about one new insertion per litter. Approximately 50% of the insertions occurred in introns. Chimeric transcripts containing endogenous and gene trap sequences were identified in Gabrb1 mutant rats. This mutagenesis system based on simple crosses and visual genotyping can be used to generate a collection of single-gene mutations in the rat. PMID:23023007

  18. BAC modification through serial or simultaneous use of CRE/Lox technology.

    PubMed

    Parrish, Mark; Unruh, Jay; Krumlauf, Robb

    2011-01-01

    Bacterial Artificial Chromosomes (BACs) are vital tools in mouse genomic analyses because of their ability to propagate large inserts. The size of these constructs, however, prevents the use of conventional molecular biology techniques for modification and manipulation. Techniques such as recombineering and Cre/Lox methodologies have thus become heavily relied upon for such purposes. In this work, we investigate the applicability of Lox variant sites for serial and/or simultaneous manipulations of BACs. We show that Lox spacer mutants are very specific, and inverted repeat variants reduce Lox reaction rates through reducing the affinity of Cre for the site, while retaining some functionality. Employing these methods, we produced serial modifications encompassing four independent changes which generated a mouse HoxB BAC with fluorescent reporter proteins inserted into four adjacent Hox genes. We also generated specific, simultaneous deletions using combinations of spacer variants and inverted repeat variants. These techniques will facilitate BAC manipulations and open a new repertoire of methods for BAC and genome manipulation. PMID:21197414

  19. America's Star Libraries

    ERIC Educational Resources Information Center

    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…

  20. Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata

    PubMed Central

    2014-01-01

    Background Japanese amberjack/yellowtail (Seriola quinqueradiata) is a commonly cultured marine fish in Japan. For cost effective fish production, a breeding program that increases commercially important traits is one of the major solutions. In selective breeding, information of genetic markers is useful and sufficient to identify individuals carrying advantageous traits but if the aim is to determine the genetic basis of the trait, large insert genomic DNA libraries are essential. In this study, toward prospective understanding of genetic basis of several economically important traits, we constructed a high-coverage bacterial artificial chromosome (BAC) library, obtained sequences from the BAC-end, and constructed comprehensive female and male linkage maps of yellowtail using Simple Sequence Repeat (SSR) markers developed from the BAC-end sequences and a yellowtail genomic library. Results The total insert length of the BAC library we constructed here was estimated to be approximately 11 Gb and hence 16-times larger than the yellowtail genome. Sequencing of the BAC-ends showed a low fraction of repetitive sequences comparable to that in Tetraodon and fugu. A total of 837 SSR markers developed here were distributed among 24 linkage groups spanning 1,026.70 and 1,057.83 cM with an average interval of 4.96 and 4.32 cM in female and male map respectively without any segregation distortion. Oxford grids suggested conserved synteny between yellowtail and stickleback. Conclusions In addition to characteristics of yellowtail genome such as low repetitive sequences and conserved synteny with stickleback, our genomic and genetic resources constructed and revealed here will be powerful tools for the yellowtail breeding program and also for studies regarding the genetic basis of traits. PMID:24684753

  1. Public Libraries

    ERIC Educational Resources Information Center

    Library Journal, 1972

    1972-01-01

    Building data is given for the following public libraries: New York, New York; Blue Island, Illinois; Corte Madera, California; Muskogee, Oklahoma: Charlotte, North Carolina; Washington, D.C.; Houston, Texas; Albermarle, North Carolina; Spokane, Washington; and Hemet, California. (Author/NH)

  2. Library Venturing.

    ERIC Educational Resources Information Center

    Wilson, H. Donald

    1986-01-01

    There is opportunity for service and profit to imaginative libraries organizing to provide new forms of knowledge. Librarians as entrepreneurs must learn venture management and finance. Available assistance includes growing entrepreneural understanding in large institutions; family and friends; private wealth-seeking investment; new business…

  3. Library Handbook.

    ERIC Educational Resources Information Center

    Cupp, Christian M., Ed.

    The purpose of this handbook is to help students, staff, and community patrons attain a reasonable degree of skill in using the Southeastern Community College Library effectively. The first section instructs the user on how to find information. A discussion of the card catalog and its use provides examples of catalog cards, reviews the…

  4. Library Environment.

    ERIC Educational Resources Information Center

    Computers in Libraries, 1993

    1993-01-01

    This special section includes two articles that review products and services for the automated library environment. Highlights include ergonomic products; products for visually, hearing-, and speech-impaired users; analog film recorders; computer filters; document imaging systems; electric filing systems; and printers. A list of vendors is…

  5. Construction and characterization of bacterial artificial chromosomes (BACs) containing herpes simplex virus full-length genomes.

    PubMed

    Nagel, Claus-Henning; Pohlmann, Anja; Sodeik, Beate

    2014-01-01

    Bacterial artificial chromosomes (BACs) are suitable vectors not only to maintain the large genomes of herpesviruses in Escherichia coli but also to enable the traceless introduction of any mutation using modern tools of bacterial genetics. To clone a herpes simplex virus genome, a BAC replication origin is first introduced into the viral genome by homologous recombination in eukaryotic host cells. As part of their nuclear replication cycle, genomes of herpesviruses circularize and these replication intermediates are then used to transform bacteria. After cloning, the integrity of the recombinant viral genomes is confirmed by restriction length polymorphism analysis and sequencing. The BACs may then be used to design virus mutants. Upon transfection into eukaryotic cells new herpesvirus strains harboring the desired mutations can be recovered and used for experiments in cultured cells as well as in animal infection models. PMID:24671676

  6. BacDive – The Bacterial Diversity Metadatabase in 2016

    PubMed Central

    Söhngen, Carola; Podstawka, Adam; Bunk, Boyke; Gleim, Dorothea; Vetcininova, Anna; Reimer, Lorenz Christian; Ebeling, Christian; Pendarovski, Cezar; Overmann, Jörg

    2016-01-01

    BacDive–the Bacterial Diversity Metadatabase (http://bacdive.dsmz.de) provides strain-linked information about bacterial and archaeal biodiversity. The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. The majority of data is manually annotated and curated. Currently (with release 9/2015), BacDive covers 53 978 strains. Newly implemented RESTful web services provide instant access to the content in machine-readable XML and JSON format. Besides an overall increase of data content, BacDive offers new data fields and features, e.g. the search for gene names, plasmids or 16S rRNA in the advanced search, as well as improved linkage of entries to external life science web resources. PMID:26424852

  7. Advances in BAC-Based Physical Mapping and Map Integration Strategies in Plants

    PubMed Central

    Ariyadasa, Ruvini; Stein, Nils

    2012-01-01

    In the advent of next-generation sequencing (NGS) platforms, map-based sequencing strategy has been recently suppressed being too expensive and laborious. The detailed studies on NGS drafts alone indicated these assemblies remain far from gold standard reference quality, especially when applied on complex genomes. In this context the conventional BAC-based physical mapping has been identified as an important intermediate layer in current hybrid sequencing strategy. BAC-based physical map construction and its integration with high-density genetic maps have benefited from NGS and high-throughput array platforms. This paper addresses the current advancements of BAC-based physical mapping and high-throughput map integration strategies to obtain densely anchored well-ordered physical maps. The resulted maps are of immediate utility while providing a template to harness the maximum benefits of the current NGS platforms. PMID:22500080

  8. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals.

    PubMed

    Poser, Ina; Sarov, Mihail; Hutchins, James R A; Hériché, Jean-Karim; Toyoda, Yusuke; Pozniakovsky, Andrei; Weigl, Daniela; Nitzsche, Anja; Hegemann, Björn; Bird, Alexander W; Pelletier, Laurence; Kittler, Ralf; Hua, Sujun; Naumann, Ronald; Augsburg, Martina; Sykora, Martina M; Hofemeister, Helmut; Zhang, Youming; Nasmyth, Kim; White, Kevin P; Dietzel, Steffen; Mechtler, Karl; Durbin, Richard; Stewart, A Francis; Peters, Jan-Michael; Buchholz, Frank; Hyman, Anthony A

    2008-05-01

    The interpretation of genome sequences requires reliable and standardized methods to assess protein function at high throughput. Here we describe a fast and reliable pipeline to study protein function in mammalian cells based on protein tagging in bacterial artificial chromosomes (BACs). The large size of the BAC transgenes ensures the presence of most, if not all, regulatory elements and results in expression that closely matches that of the endogenous gene. We show that BAC transgenes can be rapidly and reliably generated using 96-well-format recombineering. After stable transfection of these transgenes into human tissue culture cells or mouse embryonic stem cells, the localization, protein-protein and/or protein-DNA interactions of the tagged protein are studied using generic, tag-based assays. The same high-throughput approach will be generally applicable to other model systems. PMID:18391959

  9. Construction and Characterization of New piggyBac Vectors for Constitutive or Inducible Expression of Heterologous Gene Pairs and the Identification of a Previously Unrecognized Activator Sequence in piggyBac

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The piggyBac transposable element was first identified when it inserted itself into baculovirus genes during infection, causing a mutant plaque morphology phenotype. Since then, piggyBac has been developed into a germline tranformation vector usable with a wide variety of organisms. In this study...

  10. Estimating Driver Risk Using Alcohol Biomarkers, Interlock BAC Tests and Psychometric Assessments: Initial Descriptives

    PubMed Central

    Marques, Paul; Tippetts, Scott; Allen, John; Javors, Martin; Alling, Christer; Yegles, Michel; Pragst, Fritz; Wurst, Friedrich

    2009-01-01

    Aim To identify alcohol biomarker and psychometric measures that relate to drivers’ blood alcohol concentration (BAC) patterns from ignition interlock devices (IIDs). Design, Setting, Participants, Measurements In Alberta, Canada, 534 drivers, convicted of driving under the influence of alcohol (DUI), installed IIDs and agreed to participate in a research study. IID BAC tests are an established proxy for predicting future DUI convictions. Three risk groups were defined by rates of failed BAC tests. Program entry and followup blood samples (n=302, 171) were used to measure phosphatidyl ethanol (PETH), carbohydrate deficient transferrin (%CDT), gamma glutamyltransferase (GGT) and other biomarkers. Program entry urine (n=130) was analyzed for ethyl glucuronide (ETG) and ethyl sulfate (ETS). Entry hair samples were tested for fatty acid ethyl esters (FAEE) (n=92) and ETG (n=146). Psychometric measures included the DSM-4 Diagnostic Interview Schedule Alcohol Module, Alcohol Use Disorders Identification Test (AUDIT), the Timeline Followback (TLFB), the Drinker Inventory of Consequences (DRINC), and the Temptation and Restraint Inventory (TRI). Findings Except for FAEE, all alcohol biomarkers were significantly related to the interlock BAC test profiles; higher marker levels predicted higher rates of interlock BAC test failures. PETH, the strongest with an overall ANOVA F ratio of 35.5, had significant correlations with all nine of the other alcohol biomarkers and with 16 of 19 psychometric variables. Urine ETG and ETS were strongly correlated with the IID BAC tests. Conclusions The findings suggest several alcohol biomarkers and assessments could play an important role in the prediction and control of driver alcohol risk when relicensing. PMID:19922520

  11. Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice.

    PubMed

    Jakse, Jernej; Telgmann, Alexa; Jung, Christian; Khar, Anil; Melgar, Sergio; Cheung, Foo; Town, Christopher D; Havey, Michael J

    2006-12-01

    The Poales (includes the grasses) and Asparagales [includes onion (Allium cepa L.) and asparagus (Asparagus officinalis L.)] are the two most economically important monocot orders. The Poales are a member of the commelinoid monocots, a group of orders sister to the Asparagales. Comparative genomic analyses have revealed a high degree of synteny among the grasses; however, it is not known if this synteny extends to other major monocot groups such as the Asparagales. Although we previously reported no evidence for synteny at the recombinational level between onion and rice, microsynteny may exist across shorter genomic regions in the grasses and Asparagales. We sequenced nine asparagus BACs to reveal physically linked genic-like sequences and determined their most similar positions in the onion and rice genomes. Four of the asparagus BACs were selected using molecular markers tightly linked to the sex-determining M locus on chromosome 5 of asparagus. These BACs possessed only two putative coding regions and had long tracts of degenerated retroviral elements and transposons. Five asparagus BACs were selected after hybridization of three onion cDNAs that mapped to three different onion chromosomes. Genic-like sequences that were physically linked on the cDNA-selected BACs or genetically linked on the M-linked BACs showed significant similarities (e < -20) to expressed sequences on different rice chromosomes, revealing no evidence for microsynteny between asparagus and rice across these regions. Genic-like sequences that were linked in asparagus were used to identify highly similar (e < -20) expressed sequence tags (ESTs) of onion. These onion ESTs mapped to different onion chromosomes and no relationship was observed between physical or genetic linkages in asparagus and genetic linkages in onion. These results further indicate that synteny among grass genomes does not extend to a sister order in the monocots and that asparagus may not be an appropriate smaller genome

  12. GISH and BAC-FISH study of apomictic Beta M14.

    PubMed

    Ge, Yan; He, GuangChun; Wang, ZhiWei; Guo, DeDong; Qin, Rui; Li, RongTian

    2007-04-01

    Apomixis is a means of asexual reproduction by which plants produce embryos without fertilization and meiosis, therefore the embryo is of clonal and maternal origin. Interspecific hybrids between diploid B. vulgaris (2n=2x=18) and tetraploid B. corolliflora (2n=4x=36) were established, and then back-crossed with B. vulgaris. Among their offspring, monosomic addition line M14 (2n=2x=18+1) was selected because of the apomictic phenotype. We documented chromosome transmission from B. corolliflora into M14 by using genomic in situ hybridization (GISH). Suppression of cross-hybridization by blocking DNA was not necessary, indicating that the investigated Beta genome contains sufficient species-specific DNA, thus enabling the determination of genomic composition of the hybrids. We analyzed BAC microarrays of B. corolliflora chromosome 9 by using fluorescence-specific mRNA of B. vulgaris and Beta M14. BAC clones 16-M11 and 26-L15 were detected as fluorescence-specifics of BAC DNA of Beta M14. Then both BAC clones 16-M11 and 26-L15 were in situ hybridized to M14 chromosomes. The two hybridized BAC clones were located close to the telomere region of the long arm of a single chromosome 9, and showed hemizygosity. The results of BAC microarrays showed that these developments of embryo and endosperm have conservative expression patterns, indicating that sexual reproduction and apomixis have an interrelated pathway with common regulatory components and that the induction of a modified sexual reproduction program may enable the manifestation of apomixis in Beta species. It would be sufficient for the expression of apomixes with those apomictic-specific genes on chromosome 9 of B. corolliflora. PMID:17447032

  13. BacM, an N-terminally processed bactofilin of Myxococcus xanthus, is crucial for proper cell shape

    PubMed Central

    Koch, Matthias K.; McHugh, Colleen A.; Hoiczyk, Egbert

    2011-01-01

    Summary Bactofilins are fibre-forming bacterial cytoskeletal proteins. Here, we report the structural and biochemical characterization of MXAN_7475 (BacM), one of the four bactofilins of Myxococcus xanthus. Absence of BacM leads to a characteristic ‘crooked’ cell morphology and an increased sensitivity to antibiotics targeting cell wall biosynthesis. The absence of the other three bactofilins MXAN_4637–4635 (BacN-P) has no obvious phenotype. In M. xanthus, BacM exists as a 150-amino-acid full-length version and as a version cleaved before Ser28. In the cell, native BacM forms 3 nm wide fibres, which assemble into bundles forming helix-like cytoplasmic cables throughout the cell, and in a subset of cells additionally a polarly arranged lateral rod-like structure. Isolated fibres consist almost completely of the N-terminally truncated version, suggesting that the proteolytic cleavage occurs before or during fibre formation. Fusion of BacM to mCherry perturbs BacM function and cellular fibre arrangement, resulting for example in the formation of one prominent polar corkscrew-like structure per cell. Immunofluorescence staining of BacM and MreB shows that their cellular distributions are not matching. Taken together, these data suggest that rod-shaped bacteria like M. xanthus use bactofilin fibres to achieve and maintain their characteristic cell morphology and cell wall stability. PMID:21414039

  14. Suppression of the toxicity of Bac7 (1-35), a bovine peptide antibiotic, and its production in E. coli.

    PubMed

    Ishida, Yojiro; Inouye, Masayori

    2016-03-01

    Bac7 (1-35) is an Arg- and Pro-rich peptide antibiotic, produced in bovine cells to protect them from microbial infection. It has been demonstrated to inhibit the protein synthesis in E. coli, leading to cell death. Because of its toxicity, no cost effective methods have been developed for Bac7 production in Escherichia coli for its potential clinical use. Here, we found a method to suppress Bac7 (1-35) toxicity in E. coli to establish its high expression system, in which Bac7 (1-35) was fused to the C-terminal end of protein S, a major spore-coat protein from Myxococcus xanthus, using a linker containing a Factor Xa cleavage site. The resulting His6-PrS2-Bac7 (1-35) (PrS2 is consisted of two N-terminal half domains of protein S connected in tandem) was well expressed using the Single-Protein Production (SPP) system at low temperature and subsequently purified in a single step by using a Ni column. The combination of protein S fusion and its expression in the SPP system at low temperature appeared to suppress Bac7 (1-35) toxicity. Both the purified His6-PrS2-Bac7 (1-35) and His6-PrS2-Bac7 (1-35) treated by Factor Xa were proven to be a potent inhibitor for cell-free protein synthesis. PMID:26936849

  15. BacM, an N-terminally processed bactofilin of Myxococcus xanthus, is crucial for proper cell shape.

    PubMed

    Koch, Matthias K; McHugh, Colleen A; Hoiczyk, Egbert

    2011-05-01

    Bactofilins are fibre-forming bacterial cytoskeletal proteins. Here, we report the structural and biochemical characterization of MXAN_7475 (BacM), one of the four bactofilins of Myxococcus xanthus. Absence of BacM leads to a characteristic 'crooked' cell morphology and an increased sensitivity to antibiotics targeting cell wall biosynthesis. The absence of the other three bactofilins MXAN_4637-4635 (BacN-P) has no obvious phenotype. In M. xanthus, BacM exists as a 150-amino-acid full-length version and as a version cleaved before Ser28. In the cell, native BacM forms 3 nm wide fibres, which assemble into bundles forming helix-like cytoplasmic cables throughout the cell, and in a subset of cells additionally a polarly arranged lateral rod-like structure. Isolated fibres consist almost completely of the N-terminally truncated version, suggesting that the proteolytic cleavage occurs before or during fibre formation. Fusion of BacM to mCherry perturbs BacM function and cellular fibre arrangement, resulting for example in the formation of one prominent polar corkscrew-like structure per cell. Immunofluorescence staining of BacM and MreB shows that their cellular distributions are not matching. Taken together, these data suggest that rod-shaped bacteria like M. xanthus use bactofilin fibres to achieve and maintain their characteristic cell morphology and cell wall stability. PMID:21414039

  16. Library Automation and Library Education.

    ERIC Educational Resources Information Center

    Drabenstott, Jon, Ed.

    1987-01-01

    Several consultants address the issue of competencies required of professional librarians for the effective management of the automation process. Highlights include formal and professional ongoing education and the need for technical training and problem solving skills to enable librarians to evaluate and develop library systems effectively.…

  17. High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization.

    PubMed

    Jönsson, Göran; Staaf, Johan; Olsson, Eleonor; Heidenblad, Markus; Vallon-Christersson, Johan; Osoegawa, Kazutoyo; de Jong, Pieter; Oredsson, Stina; Ringnér, Markus; Höglund, Mattias; Borg, Ake

    2007-06-01

    A BAC-array platform for comparative genomic hybridization was constructed from a library of 32,433 clones providing complete genome coverage, and evaluated by screening for DNA copy number changes in 10 breast cancer cell lines (BT474, MCF7, HCC1937, SK-BR-3, L56Br-C1, ZR-75-1, JIMT1, MDA-MB-231, MDA-MB-361, and HCC2218) and one cell line derived from fibrocystic disease of the breast (MCF10A). These were also characterized by gene expression analysis and found to represent all five recently described breast cancer subtypes using the "intrinsic gene set" and centroid correlation. Three cell lines, HCC1937 and L56BrC1 derived from BRCA1 mutation carriers and MDA-MB-231, were of basal-like subtype and characterized by a high frequency of low-level gains and losses of typical pattern, including limited deletions on 5q. Four estrogen receptor positive cell lines were of luminal A subtype and characterized by a different pattern of aberrations and high-level amplifications, including ERBB2 and other 17q amplicons in BT474 and MDA-MB-361. SK-BR-3 cells, characterized by a complex genome including ERBB2 amplification, massive high-level amplifications on 8q and a homozygous deletion of CDH1 at 16q22, had an expression signature closest to luminal B subtype. The effects of gene amplifications were verified by gene expression analysis to distinguish targeted genes from silent amplicon passengers. JIMT1, derived from an ERBB2 amplified trastuzumab resistant tumor, was of the ERBB2 subtype. Homozygous deletions included other known targets such as PTEN (HCC1937) and CDKN2A (MDA-MB-231, MCF10A), but also new candidate suppressor genes such as FUSSEL18 (HCC1937) and WDR11 (L56Br-C1) as well as regions without known genes. The tiling BAC-arrays constitute a powerful tool for high-resolution genomic profiling suitable for cancer research and clinical diagnostics. PMID:17334996

  18. Biomedical applications and studies of molecular evolution: a proposal for a primate genomic library resource.

    PubMed

    Eichler, Evan E; DeJong, Pieter J

    2002-05-01

    The anticipated completion of two of the most biomedically relevant genomes, mouse and human, within the next three years provides an unparalleled opportunity for the large-scale exploration of genome evolution. Targeted sequencing of genomic regions in a panel of primate species and comparison to reference genomes will provide critical insight into the nature of single-base pair variation, mechanisms of chromosomal rearrangement, patterns of selection, and species adaptation. Although not recognized as model "genetic organisms" because of their longevity and low fecundity, 30 of the approximately 300 primate species are targets of biomedical research. The existence of a human reference sequence and genomic primate BAC libraries greatly facilitates the recovery of genes/genomic regions of high biological interest because of an estimated maximum neutral nucleotide sequence divergence of 25%. Primate species, therefore, may be regarded as the ideal model "genomic organisms". Based on existing BAC library resources, we propose the construction of a panel of primate BAC libraries from phylogenetic anchor species for the purpose of comparative medicine as well as studies of genome evolution. PMID:11997334

  19. Symposium on Presidential Libraries.

    ERIC Educational Resources Information Center

    Relyea, Harold C.; And Others

    1994-01-01

    Includes five articles that discuss presidential libraries. Highlights include an overview of the development of the federal presidential library system; the Ronald Reagan library; the Richard Nixon library archives; access at the Gerald Ford library; and computerizing the Jimmy Carter library. (LRW)

  20. Turkish Libraries: Historical Context.

    ERIC Educational Resources Information Center

    Cakin, Irfan

    1984-01-01

    Summary of the development of libraries in Turkey highlights the existence of libraries in the ninth century, the Shamssaddin Altunaba Medrese library in Konya, libraries established during the Ottoman era, reports to reform libraries (1869-70, 1909), and reports and library developments attributed to the Republican Era beginning in 1923. (EJS)

  1. Library Research and Statistics.

    ERIC Educational Resources Information Center

    Lynch, Mary Jo; St. Lifer, Evan; Halstead, Kent; Fox, Bette-Lee; Miller, Marilyn L.; Shontz, Marilyn L.

    2001-01-01

    These nine articles discuss research and statistics on libraries and librarianship, including libraries in the United States, Canada, and Mexico; acquisition expenditures in public, academic, special, and government libraries; price indexes; state rankings of public library data; library buildings; expenditures in school library media centers; and…

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

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Zhang, Xiaojun; Scheuring, Chantel F.; Zhang, Hongbin; Li, Fuhua; Xiang, Jianhai

    2008-05-01

    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 53 760 clones while the Mbo I library consisted of 7 680clones. 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. Sperm-mediated transgenesis in chicken using a PiggyBac transposon system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sperm-mediated transgenesis in chicken using a PiggyBac transposon system Emmanuel Quansah1,2, Julie Long2, David Donovan2, Stephen Becker2, Bhanu Telugu2, Juli Frey2, Nigel Urwin1 1,Charles Sturt University, Graham Center of Agricultural Innovation, Wagga Wagga. Australia and 2Beltsville Agricultu...

  4. Insect transformation with piggyBac: getting the number of injections just right.

    PubMed

    Gregory, M; Alphey, L; Morrison, N I; Shimeld, S M

    2016-06-01

    The insertion of exogenous genetic cargo into insects using transposable elements is a powerful research tool with potential applications in meeting food security and public health challenges facing humanity. piggyBac is the transposable element most commonly utilized for insect germline transformation. The described efficiency of this process is variable in the published literature, and a comprehensive review of transformation efficiency in insects is lacking. This study compared and contrasted all available published data with a comprehensive data set provided by a biotechnology group specializing in insect transformation. Based on analysis of these data, with particular focus on the more complete observational data from the biotechnology group, we designed a decision tool to aid researchers' decision-making when using piggyBac to transform insects by microinjection. A combination of statistical techniques was used to define appropriate summary statistics of piggyBac transformation efficiency by species and insect order. Publication bias was assessed by comparing the data sets. The bias was assessed using strategies co-opted from the medical literature. The work culminated in building the Goldilocks decision tool, a Markov-Chain Monte-Carlo simulation operated via a graphical interface and providing guidance on best practice for those seeking to transform insects using piggyBac. PMID:27027400

  5. An integrated BAC/BIBAC-based physical and genetic map of the cotton genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Integrated genome-wide genetic and physical maps are crucial to many aspects of cotton genome research. We report a genome-wide BAC/BIBAC-based physical and genetic map of the upland cotton genome using a high-resolution and high-throughput capillary-based fingerprinting method. The map was constr...

  6. Chromosome evolution in Solanum traced by cross-species BAC-FISH.

    PubMed

    Szinay, Dóra; Wijnker, Erik; van den Berg, Ronald; Visser, Richard G F; de Jong, Hans; Bai, Yuling

    2012-08-01

    Chromosomal rearrangements are relatively rare evolutionary events and can be used as markers to study karyotype evolution. This research aims to use such rearrangements to study chromosome evolution in Solanum. Chromosomal rearrangements between Solanum crops and several related wild species were investigated using tomato and potato bacterial artificial chromosomes (BACs) in a multicolour fluorescent in situ hybridization (FISH). The BACs selected are evenly distributed over seven chromosomal arms containing inversions described in previous studies. The presence/absence of these inversions among the studied Solanum species were determined and the order of the BAC-FISH signals was used to construct phylogenetic trees.Compared with earlier studies, data from this study provide support for the current grouping of species into different sections within Solanum; however, there are a few notable exceptions, such as the tree positions of S. etuberosum (closer to the tomato group than to the potato group) and S. lycopersicoides (sister to S. pennellii). These apparent contradictions might be explained by interspecific hybridization events and/or incomplete lineage sorting. This cross-species BAC painting technique provides unique information on genome organization, evolution and phylogenetic relationships in a wide variety of species. Such information is very helpful for introgressive breeding. PMID:22686400

  7. Evolution of sex chromosomes ZW of Schistosoma mansoni inferred from chromosome paint and BAC mapping analyses.

    PubMed

    Hirai, Hirohisa; Hirai, Yuriko; LoVerde, Philip T

    2012-12-01

    Chromosomes of schistosome parasites among digenetic flukes have a unique evolution because they exhibit the sex chromosomes ZW, which are not found in the other groups of flukes that are hermaphrodites. We conducted molecular cytogenetic analyses for investigating the sex chromosome evolution using chromosome paint analysis and BAC clones mapping. To carry this out, we developed a technique for making paint probes of genomic DNA from a single scraped chromosome segment using a chromosome microdissection system, and a FISH mapping technique for BAC clones. Paint probes clearly identified each of the 8 pairs of chromosomes by a different fluorochrome color. Combination analysis of chromosome paint analysis with Z/W probes and chromosome mapping with 93 BAC clones revealed that the W chromosome of Schistosoma mansoni has evolved by at least four inversion events and heterochromatinization. Nine of 93 BAC clones hybridized with both the Z and W chromosomes, but the locations were different between Z and W chromosomes. The homologous regions were estimated to have moved from the original Z chromosome to the differentiated W chromosome by three inversions events that occurred before W heterohcromatinization. An inversion that was observed in the heterochromatic region of the W chromosome likely occurred after W heterochromatinization. These inversions and heterochromatinization are hypothesized to be the key factors that promoted the evolution of the W chromosome of S. mansoni. PMID:22831897

  8. C9ORF72-ALS/FTD: Transgenic Mice Make a Come-BAC.

    PubMed

    Hayes, Lindsey R; Rothstein, Jeffrey D

    2016-05-01

    For five years, since the landmark discovery of the C9ORF72 hexanucleotide repeat expansion in ALS/FTD, a transgenic mouse model has remained elusive. Now, two laboratories (Liu et al., 2016; Jiang et al., 2016) report the development of BAC transgenic mice that recapitulate features of the human disease. PMID:27151634

  9. BAC-pool 454-sequencing: A rapid and efficient approach to sequence complex tetraploid cotton genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New and emerging next generation sequencing technologies have been promising in reducing sequencing costs, but not significantly for complex polyploid plant genomes such as cotton. Large and highly repetitive genome of G. hirsutum (~2.5GB) is less amenable and cost-intensive with traditional BAC-by...

  10. Genetic transformation mediated by piggyBac in the Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Asian corn borer, Ostrinia furnacalis, is a serious pest of corn, sorghum and cotton in China and other Asian countries. The present study is the first attempt to establish the transgenic line in O. furnacalis using a piggyBac transposon, which will shed light on the future genetic control of O....

  11. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due in part to its small genome (~350 Mb), Brachypodium distachyon is emerging as a model system for temperate grasses, including important crops like wheat and barley. We present the analysis of 10.9% of the Brachypodium genome based on 64,696 BAC end sequences (BES). Analysis of repeat DNA content...

  12. BAC and Beer: Operationalizing Drunk Driving Laws in a Research Methods Course Exercise.

    ERIC Educational Resources Information Center

    Taylor, Ralph B.; McConnell, Patrick

    2001-01-01

    Focuses on an exercise utilized in a research methods class and based on social problems that invites student interest. Explains the exercise has students determine their blood alcohol level (BAC) by asking them to estimate the number of beers it would take to have them just reach driving under the influence (DUI) status. (CMK)

  13. Genetic Transformation of the Codling Moth, Cydia pomonella L., with piggyBac EGFP

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic transformation of the codling moth, Cydia pomonella, was accomplished through embryo microinjection with a plasmid-based piggyBac vector containing the enhanced green fluorescent protein (EGFP) gene. Sequencing of the flanking regions around the inserted construct results in identification o...

  14. A PiggyBac-mediated approach for muscle gene transfer or cell therapy.

    PubMed

    Ley, Déborah; Van Zwieten, Ruthger; Puttini, Stefania; Iyer, Pavithra; Cochard, Alessia; Mermod, Nicolas

    2014-11-01

    An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies. PMID:25310255

  15. Analysis Of Papaya BAC End Sequences: Insights Into The Organization Of A Tree Fruit Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Papaya (Carica papaya L.) is a major tree fruit crop of tropical and subtropical regions with an estimated genome size of 372 Mbp. We present the analysis of 4.7% of the papaya genome based on BAC end sequences (BESs) representing 17 million high-quality bases. Microsatellites discovered in 5,452 BE...

  16. Assembly and sorting of homologous BAC contigs in allotetraploid cotton genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Upland cotton (G. hirsutum) is a diploidized allopolyploid species containing At and Dt sub-genomes that have partial homology. Assembly and sorting of homologous BAC contigs into their subgenomes and further to individual chromosomes are of both great interest and great challenge for genome-wide i...

  17. BacWGSTdb, a database for genotyping and source tracking bacterial pathogens

    PubMed Central

    Ruan, Zhi; Feng, Ye

    2016-01-01

    Whole genome sequencing has become one of the routine methods in molecular epidemiological practice. In this study, we present BacWGSTdb (http://bacdb.org/BacWGSTdb), a bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. This database borrows the population structure from the current multi-locus sequence typing (MLST) scheme and adopts a hierarchical data structure: species, clonal complex and isolates. When users upload the pre-assembled genome sequences to BacWGSTdb, it offers the functionality of bacterial genotyping at both traditional MLST and whole-genome levels. More importantly, users are told which isolates in the public database are phylogenetically close to the query isolate, along with their clinical information such as host, isolation source, disease, collection time and geographical location. In this way, BacWGSTdb offers a rapid and convenient platform for worldwide users to address a variety of clinical microbiological issues such as source tracking bacterial pathogens. PMID:26433226

  18. Insect transformation with piggyBac: getting the number of injections just right

    PubMed Central

    Morrison, N. I.; Shimeld, S. M.

    2016-01-01

    Abstract The insertion of exogenous genetic cargo into insects using transposable elements is a powerful research tool with potential applications in meeting food security and public health challenges facing humanity. piggyBac is the transposable element most commonly utilized for insect germline transformation. The described efficiency of this process is variable in the published literature, and a comprehensive review of transformation efficiency in insects is lacking. This study compared and contrasted all available published data with a comprehensive data set provided by a biotechnology group specializing in insect transformation. Based on analysis of these data, with particular focus on the more complete observational data from the biotechnology group, we designed a decision tool to aid researchers' decision‐making when using piggyBac to transform insects by microinjection. A combination of statistical techniques was used to define appropriate summary statistics of piggyBac transformation efficiency by species and insect order. Publication bias was assessed by comparing the data sets. The bias was assessed using strategies co‐opted from the medical literature. The work culminated in building the Goldilocks decision tool, a Markov‐Chain Monte‐Carlo simulation operated via a graphical interface and providing guidance on best practice for those seeking to transform insects using piggyBac. PMID:27027400

  19. Strengthening State Library Administrative Agency (Territorial Library).

    ERIC Educational Resources Information Center

    Nieves M. Flores Memorial Library, Agana, Guam.

    This document describes the Basic State Plan Amendments for the Library Services and Construction Act in Guam and the regulations promulgated thereunder. The major projects described under the plan are: Strengthening State Library Administrative Agency; Staff Development; Library Collections, Extention Services, Institutional Libraries; and…

  20. Library Instruction Assessment in Academic Libraries

    ERIC Educational Resources Information Center

    Tancheva, Kornelia; Andrews, Camille; Steinhart, Gail

    2007-01-01

    Determining the best methods of assessment for a library instruction program in a large research university can be a challenging task. Albert R. Mann Library at Cornell University Library has pilot-tested three methods of formative and summative assessment for its library instruction program--attitudinal, outcomes-based, and gap-measure--and…

  1. Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase

    PubMed Central

    Manat, Guillaume; El Ghachi, Meriem; Auger, Rodolphe; Baouche, Karima; Olatunji, Samir; Kerff, Frédéric; Touzé, Thierry; Mengin-Lecreulx, Dominique; Bouhss, Ahmed

    2015-01-01

    Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP) phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2) catalyze the dephosphorylation of C55-PP molecules on the same (outer) side of the plasma membrane. PMID:26560897

  2. Cell Libraries

    NASA Technical Reports Server (NTRS)

    1994-01-01

    A NASA contract led to the development of faster and more energy efficient semiconductor materials for digital integrated circuits. Gallium arsenide (GaAs) conducts electrons 4-6 times faster than silicon and uses less power at frequencies above 100-150 megahertz. However, the material is expensive, brittle, fragile and has lacked computer automated engineering tools to solve this problem. Systems & Processes Engineering Corporation (SPEC) developed a series of GaAs cell libraries for cell layout, design rule checking, logic synthesis, placement and routing, simulation and chip assembly. The system is marketed by Compare Design Automation.

  3. [Identification of chromosomal aberration in esophageal cancer cells by mixed BAC DNA probes of chromosome arms and regions].

    PubMed

    Jiajie, Hao; Chunli, Wang; Wenyue, Gu; Xiaoyu, Cheng; Yu, Zhang; Xin, Xu; Yan, Cai; Mingrong, Wang

    2014-06-01

    Chromosomal aberration is an important genetic feature of malignant tumor cells. This study aimed to clarify whether BAC DNA could be used to identify chromosome region and arm alterations. For each chromosome region, five to ten 1 Mb BAC DNA clones were selected to construct mixed BAC DNA clones for the particular region. All of the mixed clones from regions which could cover the whole chromosome arm were then mixed to construct mixed BAC DNA clones for the arms. Mixed BAC DNA probes of arms and regions were labeled by degenerate oligonucleotide primed PCR (DOP-PCR) and Nick translation techniques, respectively. The specificities of these probes were validated by fluorescence in situ hybridization (FISH) on the metaphase chromosomes of normal human peripheral blood lymphocytes. FISH with arm-specific mixed BAC DNA probes showed that chromosomal rearrangements and involved chromosome arms were confirmed in several esophageal cancer cells. By using region-specific mixed probes, the breakpoint on 1q from the derivative chromosome t(1q;7q) was identified in 1q32-q41 in esophageal KYSE140 cells. In conclusion, we established an effective labeling method for 1 Mb BAC DNA mixed clone probes, and chromosome arm and region rearrangements could be identified in several esophageal cancer cells by using these probes. Our study provides a more precise method for identification of chromosomal aberration by M-FISH, and the established method may also be applied to the karyotype analysis of hematological malignancies and prenatal diagnosis. PMID:24929514

  4. The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.

    PubMed

    Li, Meng Amy; Pettitt, Stephen J; Eckert, Sabine; Ning, Zemin; Rice, Stephen; Cadiñanos, Juan; Yusa, Kosuke; Conte, Nathalie; Bradley, Allan

    2013-04-01

    The DNA transposon piggyBac is widely used as a tool in mammalian experimental systems for transgenesis, mutagenesis, and genome engineering. We have characterized genome-wide insertion site preferences of piggyBac by sequencing a large set of integration sites arising from transposition from two separate genomic loci and a plasmid donor in mouse embryonic stem cells. We found that piggyBac preferentially integrates locally to the excision site when mobilized from a chromosomal location and identified other nonlocal regions of the genome with elevated insertion frequencies. piggyBac insertions were associated with expressed genes and markers of open chromatin structure and were excluded from heterochromatin. At the nucleotide level, piggyBac prefers to insert into TA-rich regions within a broader GC-rich context. We also found that piggyBac can insert into sites other than its known TTAA insertion site at a low frequency (2%). Such insertions introduce mismatches that are repaired with signatures of host cell repair pathways. Transposons could be mobilized from plasmids with the observed noncanonical flanking regions, indicating that piggyBac could generate point mutations in the genome. PMID:23358416

  5. The piggyBac Transposon Displays Local and Distant Reintegration Preferences and Can Cause Mutations at Noncanonical Integration Sites

    PubMed Central

    Li, Meng Amy; Pettitt, Stephen J.; Eckert, Sabine; Ning, Zemin; Rice, Stephen; Cadiñanos, Juan; Yusa, Kosuke; Conte, Nathalie

    2013-01-01

    The DNA transposon piggyBac is widely used as a tool in mammalian experimental systems for transgenesis, mutagenesis, and genome engineering. We have characterized genome-wide insertion site preferences of piggyBac by sequencing a large set of integration sites arising from transposition from two separate genomic loci and a plasmid donor in mouse embryonic stem cells. We found that piggyBac preferentially integrates locally to the excision site when mobilized from a chromosomal location and identified other nonlocal regions of the genome with elevated insertion frequencies. piggyBac insertions were associated with expressed genes and markers of open chromatin structure and were excluded from heterochromatin. At the nucleotide level, piggyBac prefers to insert into TA-rich regions within a broader GC-rich context. We also found that piggyBac can insert into sites other than its known TTAA insertion site at a low frequency (2%). Such insertions introduce mismatches that are repaired with signatures of host cell repair pathways. Transposons could be mobilized from plasmids with the observed noncanonical flanking regions, indicating that piggyBac could generate point mutations in the genome. PMID:23358416

  6. Sustained high level transgene expression in mammalian cells mediated by the optimized piggyBac transposon system

    PubMed Central

    Chen, Xiang; Cui, Jing; Yan, Zhengjian; Zhang, Hongmei; Chen, Xian; Wang, Ning; Shah, Palak; Deng, Fang; Zhao, Chen; Geng, Nisha; Li, Melissa; Denduluri, Sahitya K.; Haydon, Rex C.; Luu, Hue H.; Reid, Russell R.; He, Tong-Chuan

    2015-01-01

    Sustained, high level transgene expression in mammalian cells, especially stem cells, may be desired in many cases for studying gene functions. Traditionally, stable transgene expression has been accomplished by using retroviral or lentiviral vectors. However, such viral vector-mediated transgene expression is often at low levels and can be reduced over time due to low copy numbers and/or chromatin remodeling repression. The piggyBac transposon has emerged as a promising non-viral vector system for efficient gene transfer into mammalian cells. Despite its inherent advantages over lentiviral and retroviral systems, piggyBac system has not been widely used, at least in part due to the limited availability of piggyBac vectors with manipulation flexibilities. Here, we seek to optimize piggyBac-mediated transgene expression and generate a more efficient, user-friendly piggyBac system. By engineering a panel of versatile piggyBac vectors and constructing recombinant adenoviruses expressing piggyBac transposase (PBase), we demonstrate that adenovirus-mediated PBase expression significantly enhances the integration efficiency and expression level of transgenes in mesenchymal stem cells and osteosarcoma cells, compared to that obtained from co-transfection of the CMV-PBase plasmid. We further determine the drug selection timeline to achieve optimal stable transgene expression. Moreover, we demonstrate that the transgene copy number of piggyBac-mediated integration is approximately 10 times higher than that mediated by retroviral vectors. Using the engineered tandem expression vector, we show that three transgenes can be simultaneously expressed in a single vector with high efficiency. Thus, these results strongly suggest that the optimized piggyBac system is a valuable tool for making stable cell lines with sustained, high transgene expression. PMID:25815368

  7. Library Services. Miscellaneous Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    Papers on library journal cooperation, interlibrary lending, library services to minorities, and school library media centers, which were presented at the 1983 International Federation of Library Associations (IFLA) conference, include: (1) "The Co-operation between Editors of Library Journals in Socialist Countries," in which Wolfgang Korluss…

  8. Marketing the Virtual Library

    ERIC Educational Resources Information Center

    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…

  9. Library Research and Statistics.

    ERIC Educational Resources Information Center

    Lynch, Mary Jo; Brier, David J.; Lebbin, Vickery K.; Halstead, Kent; Fox, Bette-Lee; Kremen, Maya L.; Miller, Marilyn L.; Shontz, Marilyn L.

    1998-01-01

    Provides nine articles: research on libraries and librarianship, 1997; changing faces of library education (ALA-accredited graduate program title changes); number of libraries in the U.S., Canada, and Mexico; highlights of NCES surveys; library acquisition expenditures; price indexes for public and academic libraries; state rankings of selected…

  10. Library Handbook for Faculty.

    ERIC Educational Resources Information Center

    Martinez, Angelina, Ed.

    Discussions of library resources, services and related activities as well as library materials selection and acquisition are provided for faculty to facilitate and enhance their use of the library. Included in the library resources section are books, periodicals, microforms, and special collections and archives. Instruction in library use,…

  11. Library Directions in 1988.

    ERIC Educational Resources Information Center

    DeCandido, GraceAnne A.

    1989-01-01

    Reviews major library issues and events of 1988, including: (1) the Federal Bureau of Investigation's Library Awareness Program; (2) cooperation with USSR libraries; (3) library finance; (4) preservation; and (5) special programing. News about a number of prominent library professionals is included in a sidebar. (MES)

  12. Public Library in Thailand.

    ERIC Educational Resources Information Center

    Lerdsuriyakul, Kulthorn

    This paper on public libraries in Thailand begins with a section that provides background on public libraries in the past, lists the functions of the public library, and describes three size classifications of public libraries. The second section outlines the tasks of the current public library in three areas: informal education; nonformal…

  13. Application of DNA microarray for screening metagenome library clones.

    PubMed

    Park, Soo-Je; Chae, Jong-Chan; Rhee, Sung-Keun

    2010-01-01

    Sequence-based screening tools of a metagenome library can expedite metagenome researches considering tremendous metagenome diversities. Several critical disadvantages of activity-based screening of metagenome libraries could be overcome by sequence-based screening approaches. DNA microarray technology widely used for monitoring environmental genes can be employed for screening environmental fosmid and BAC clones harboring target genes due to its high throughput nature. DNAs of fosmid clones are extracted and spotted on a glass slide and fluorescence-labeled probes are hybridized to the microarray. Specific hybridization signals can be obtained only for the fosmid clones that contain the target gene with high sensitivity (10 ng/μL of fosmid clone DNA) and quantitativeness. PMID:20830574

  14. Homecoming for Library Symbol.

    ERIC Educational Resources Information Center

    Egan, Bessie

    1987-01-01

    Discusses the significance and development of the library symbol and the history of its acceptance by the American Library Association (ALA) and the Canadian Library Association (CLA). Suggestions are made for its use. (CLB)

  15. Karyotyping of Brachypodium pinnatum (2n = 18) chromosomes using cross-species BAC-FISH.

    PubMed

    Wolny, Elzbieta; Fidyk, Wojciech; Hasterok, Robert

    2013-04-01

    Identification of individual chromosomes in a complement is usually a difficult task in the case of most plant species, especially for those with small, numerous, and morphologically uniform chromosomes. In this paper, we demonstrate that the landmarks produced by cross-species fluorescence in situ hybridisation (FISH) of Brachypodium distachyon derived bacterial artificial chromosome (BAC) clones can be used for discrimination of Brachypodium pinnatum (2n = 18) chromosomes. Selected sets of clones were hybridised in several sequential experiments performed on exactly the same chromosome spreads, using reprobing of cytological preparations. Analysis of the morphometric features of B. pinnatum chromosomes was performed to establish their total length, the position of centromeres, and the position of BAC-based landmarks in relation to the centromere, thereby enabling their effective karyotyping, which is a prerequisite for more complex study of the grass genome structure and evolution at the cytomolecular level. PMID:23706077

  16. Structural identification of DnaK binding sites within bovine and sheep bactenecin Bac7.

    PubMed

    Zahn, Michael; Kieslich, Bjorn; Berthold, Nicole; Knappe, Daniel; Hoffmann, Ralf; Strater, Norbert

    2014-04-01

    Bacterial resistance against common antibiotics is an increasing health problem. New pharmaceuticals for the treatment of infections caused by resistant pathogens are needed. Small proline-rich antimicrobial peptides (PrAMPs) from insects are known to bind intracellularly to the conventional substrate binding cleft of the E. coli Hsp70 chaperone DnaK. Furthermore, bactenecins from mammals, members of the cathelicidin family, also contain potential DnaK binding sites. Crystal structures of bovine and sheep Bac7 in complex with the DnaK substrate binding domain show that the peptides bind in the forward binding mode with a leucine positioned in the central hydrophobic pocket. In most structures, proline and arginine residues preceding leucine occupy the hydrophobic DnaK binding sites -1 and -2. Within bovine Bac7, four potential DnaK binding sites were identified. PMID:24164259

  17. Mobilization of giant piggyBac transposons in the mouse genome

    PubMed Central

    Li, Meng Amy; Turner, Daniel J.; Ning, Zemin; Yusa, Kosuke; Liang, Qi; Eckert, Sabine; Rad, Lena; Fitzgerald, Tomas W.; Craig, Nancy L.; Bradley, Allan

    2011-01-01

    The development of technologies that allow the stable delivery of large genomic DNA fragments in mammalian systems is important for genetic studies as well as for applications in gene therapy. DNA transposons have emerged as flexible and efficient molecular vehicles to mediate stable cargo transfer. However, the ability to carry DNA fragments >10 kb is limited in most DNA transposons. Here, we show that the DNA transposon piggyBac can mobilize 100-kb DNA fragments in mouse embryonic stem (ES) cells, making it the only known transposon with such a large cargo capacity. The integrity of the cargo is maintained during transposition, the copy number can be controlled and the inserted giant transposons express the genomic cargo. Furthermore, these 100-kb transposons can also be excised from the genome without leaving a footprint. The development of piggyBac as a large cargo vector will facilitate a wider range of genetic and genomic applications. PMID:21948799

  18. Construction and characterization of a bacterial artificial chromosome library for the hexaploid wheat line 92R137.

    PubMed

    Zeng, Qingdong; Yuan, Fengping; Xu, Xin; Shi, Xue; Nie, Xiaojun; Zhuang, Hua; Chen, Xianming; Wang, Zhonghua; Wang, Xiaojie; Huang, Lili; Han, Dejun; Kang, Zhensheng

    2014-01-01

    For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from the HindIII digestion and 375,552 from the BamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from the HindIII sublibrary and 573 clones from the BamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, the HindIII sublibrary was estimated to have a 3.01-fold coverage and the BamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as gene Yr26 for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools with Xwe173, a marker tightly linked to Yr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning of Yr26 and other genes of interest. PMID:24895618

  19. Construction and Characterization of a Bacterial Artificial Chromosome Library for the Hexaploid Wheat Line 92R137

    PubMed Central

    Yuan, Fengping; Xu, Xin; Shi, Xue; Zhuang, Hua; Wang, Zhonghua; Huang, Lili; Han, Dejun; Kang, Zhensheng

    2014-01-01

    For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from the HindIII digestion and 375,552 from the BamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from the HindIII sublibrary and 573 clones from the BamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, the HindIII sublibrary was estimated to have a 3.01-fold coverage and the BamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as gene Yr26 for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools with Xwe173, a marker tightly linked to Yr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning of Yr26 and other genes of interest. PMID:24895618

  20. The Library of Virginia's Digital Library Project.

    ERIC Educational Resources Information Center

    Roderick, Elizabeth; Taylor, Jean Marie; Byrd, Sam; Courson, Glenn

    1997-01-01

    Describes The Library of Virginia's Digital Library Project that has made many of its state library collections available via the Internet and World Wide Web. Highlights include digitization decisions; the HTML Web gateway; the online catalog; microfilm digitization; users and use statistics; and future projects. (LRW)

  1. Neutralization of endotoxin in vitro and in vivo by Bac7(1-35), a proline-rich antibacterial peptide.

    PubMed

    Ghiselli, Roberto; Giacometti, Andrea; Cirioni, Oscar; Circo, Raffaella; Mocchegiani, Federico; Skerlavaj, Barbara; D'Amato, Giuseppina; Scalise, Giorgio; Zanetti, Margherita; Saba, Vittorio

    2003-06-01

    Lipopolysaccharides (LPS), or endotoxins, are structural components of gram-negative bacteria implicated in the pathogenesis of septic shock. In this study the antiendotoxin activity of Bac7(1-35), a synthetic peptide based on the sequence of a proline-rich antibacterial peptide from bovine neutrophils, was investigated in vitro and in an experimental rat model of gram-negative septic shock. The ability of Bac7(1-35) to bind LPS from Escherichia coli O111:B4 was determined using a sensitive Limulus chromogenic assay. In the in vivo study, adult male Wistar rats were given an intraperitoneal injection of 1 x 10(9) colony-forming units of E. coli ATCC 25922. All animals were randomized to receive intraperitoneally 1 mg/kg Bac7(1-35), or isotonic sodium chloride solution (control group C1), 60 mg/kg of piperacillin and 1 mg/kg polymyxin B, 1 mg/kg of polymyxin B plus 60 mg/kg of piperacillin, and 1 mg/kg of Bac7(1-35) plus 60 mg/kg of piperacillin. Each group included 15 animals. Bac7(1-35) was found to completely inhibit the LPS procoagulant activity at approximately 10 microM peptide concentration, as determined by in vitro LAL chromogenic assay. Treatment with Bac7(1-35) resulted in significant decrease in plasma endotoxin levels and lethality rates compared with saline injected control animals. No statistically significant differences were noted between Bac7(1-35) and polymyxin B in reducing all variables measured. These results provide evidence for the ability of Bac7(1-35) to effectively bind LPS and protect animals from lethal effects of this molecule, and point to its potential use for the treatment of endotoxin-induced septic shock. PMID:12785015

  2. Remobilizing deleted piggyBac vector post-integration for transgene stability in silkworm.

    PubMed

    Wang, Feng; Wang, Riyuan; Wang, Yuancheng; Xu, Hanfu; Yuan, Lin; Ding, Huan; Ma, Sanyuan; Zhou, You; Zhao, Ping; Xia, Qingyou

    2015-06-01

    Deletion of transposable elements post-genomic integration holds great promise for stability of the transgene in the host genome and has an essential role for the practical application of transgenic animals. In this study, a modified piggyBac vector that mediated deletion of the transposon sequence post-integration for transgene stability in the economically important silkworm Bombyx mori was constructed. The piggyBac vector architecture contains inversed terminal repeat sequences L1, L2 and R1, which can form L1/R1 and L2/R1 types of transposition cassettes. hsp70-PIG as the piggyBac transposase expression cassette for initial transposition, further remobilization and transgene stabilization test was transiently expressed in a helper vector or integrated into the modified vector to produce a transgenic silkworm. Shortening L2 increased the transformation frequency of L1/R1 into the silkworm genome compared to L2/R1. After the integration of L1/R1 into the genome, the remobilization of L2/R1 impaired the transposon structure and the resulting transgene linked with an impaired transposon was stable in the genome even in the presence of exogenously introduced transposase, whereas those flanked by the intact transposon were highly mobile in the genome. Our results demonstrated the feasibility of post-integration deletion of transposable elements to guarantee true transgene stabilization in silkworm. We suggest that the modified vector will be a useful resource for studies of transgenic silkworms and other piggyBac-transformed organisms. PMID:25589404

  3. Hyperactive piggyBac Gene Transfer in Human Cells and In Vivo

    PubMed Central

    Doherty, Joseph E.; Huye, Leslie E.; Yusa, Kosuke; Zhou, Liqin; Craig, Nancy L.

    2012-01-01

    Abstract We characterized a recently developed hyperactive piggyBac (pB) transposase enzyme [containing seven mutations (7pB)] for gene transfer in human cells in vitro and to somatic cells in mice in vivo. Despite a protein level expression similar to that of native pB, 7pB significantly increased the gene transfer efficiency of a neomycin resistance cassette transposon in both HEK293 and HeLa cultured human cells. Native pB and SB100X, the most active transposase of the Sleeping Beauty transposon system, exhibited similar transposition efficiency in cultured human cell lines. When delivered to primary human T cells ex vivo, 7pB increased gene delivery two- to threefold compared with piggyBac and SB100X. The activity of hyperactive 7pB transposase was not affected by the addition of a 24-kDa N-terminal tag, whereas SB100X manifested a 50% reduction in transposition. Hyperactive 7pB was compared with native pB and SB100X in vivo in mice using hydrodynamic tail-vein injection of a limiting dose of transposase DNA combined with luciferase reporter transposons. We followed transgene expression for up to 6 months and observed approximately 10-fold greater long-term gene expression in mice injected with a codon-optimized version of 7pB compared with mice injected with native pB or SB100X. We conclude that hyperactive piggyBac elements can increase gene transfer in human cells and in vivo and should enable improved gene delivery using the piggyBac transposon system in a variety of cell and gene-therapy applications. PMID:21992617

  4. piggyBac-based insertional mutagenesis in the presence of stably integrated P elements in Drosophila.

    PubMed

    Hacker, Udo; Nystedt, Sverker; Barmchi, Mojgan Padash; Horn, Carsten; Wimmer, Ernst A

    2003-06-24

    P element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for Drosophila adult viability. Mutation of all genes in the fly genome, however, poses a problem, because P elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of P element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniques are P element-based and can therefore not be combined with the use of P elements as mutagenic agents. To circumvent these limitations, we have developed an insertional mutagenesis system using non-P element transposons. An enhanced yellow fluorescent protein-marked piggyBac-based mutator element was mobilized by a piggyBac specific transposase source expressed from a Hermes-based jump-starter transposon marked with enhanced cyan fluorescent protein. In a pilot screen, we have generated 798 piggyBac insertions on FRT bearing third chromosomes of which 9% have sustained a putatively piggyBac-related lethal hit. The FRTs present on the target chromosome remained stably integrated during the screen and could subsequently be used to generate germ-line clones associated with maternal and zygotic phenotypes. PCR-based analysis of insertion loci shows that 57% of the insertions are in genes for which no P element insertions have been reported. Our data demonstrate the potential of this technique to facilitate the quest for saturation mutagenesis of the Drosophila genome. The system is Drosophila nonspecific and potentially applicable in a broad spectrum of nonmodel organisms. PMID:12802016

  5. Construction of a Rye BAC Library for Utilization in Physical Mapping of an Aluminum Tolerance Gene Complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aluminium, the most abundant metal on earth, is highly toxic to plant growth and is found in about 2.5 billion hectares of acid soils, including more than 130 million hectares in the United States. Many of the world’s farmers are living on marginal soils that offer a stressful environment for plant ...

  6. CONSTRUCTION OF A RYE CV. BLANCO BAC LIBRARY, AND PROGRESS TOWARDS CLONING THE RYE ALT3 ALUMINUM TOLERANCE GENE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In addition to being an important cereal crop, rye (Secale cereale L.) provides valuable traits for other crops, as a parent of the amphidiploid triticale, and as a donor of translocated chromosome segments in wheat. Rye possesses excellent tolerance to many biotic and abiotic stresses that could p...

  7. Alabama Public Library Service Library Directory and 1996 Statistical Report.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    This publication presents library contact information and statistics for Alabama public libraries for fiscal year 1996 (October 1, 1995-September 30, 1996). The library directory is arranged by type of library: public libraries, single-county public library systems, multi-county public library systems, and multitype library systems. Entries…

  8. Large Gap Size Paired-end Library Construction for Second Generation Sequencing

    SciTech Connect

    Peng, Ze; Hamilton, Matthew; Froula, Jeff; Ewing, Aren; Foster, Brian; Cheng, Jan-Fang

    2010-05-28

    Fosmid or BAC end sequencing plays an important role in de novo assembly of large genomes like fungi and plants. However construction and Sanger sequencing of fosmid or BAC libraries are laborious and costly. The current 454 Paired-End (PE) Library and Illumina Jumping Library construction protocols are limited with the gap sizes of approximately 20 kb and 8 kb, respectively. In the attempt to understand the limitations of constructing PE libraries with greater than 30Kb gaps, we have purified 18, 28, 45, and 65Kb sheared DNA fragments from yeast and circularized the ends using the Cre-loxP approach described in the 454 PE Library protocol. With the increasing fragment sizes, we found a general trend of decreasing library quality in several areas. First, redundant reads and reads containing multiple loxP linkers increase when the average fragment size increases. Second, the contamination of short distance pairs (<10Kb) increases as the fragment size increases. Third, chimeric rate increases with the increasing fragment sizes. We have modified several steps to improve the quality of the long span PE libraries. The modification includes (1) the use of special PFGE program to reduce small fragment contamination; (2) the increase of DNA samples in the circularization step and prior to the PCR to reduce redundant reads; and (3) the decrease of fragment size in the double SPRI size selection to get a higher frequency of LoxP linker containing reads. With these modifications we have generated large gap size PE libraries with a much better quality.

  9. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon

    PubMed Central

    Yusa, Kosuke; Rad, Roland; Takeda, Junji; Bradley, Allan

    2009-01-01

    Induced pluripotent stem cells (iPSCs) have been generated from somatic cells by transgenic expression of Oct4, Sox2, Klf4, and cMyc. A major difficulty in the application of this technology for regenerative medicine, however, is the delivery of reprogramming factors. Whereas retroviral transduction increases the risk of tumorigenicity, transient expression methods have considerably lower reprogramming efficiencies. Here we show a highly efficient piggyBac transposon-based approach to generate integration-free iPSCs. Transposons carrying 2A peptide-linked reprogramming factors induced reprogramming of mouse embryonic fibroblasts with equivalent efficiencies to retroviral transduction. Transposons were removed from these primary iPSCs by re-expressing transposase. Transgene-free iPSCs could be easily identified by HSVtk-FIAU selection. piggyBac excises without a footprint, leaving the iPSC genome without any genetic alteration. iPSCs fulfilled all criteria of pluripotency, such as expression of embryonic stem cell-specific markers, teratoma formation and contribution to chimeras. piggyBac transposon-based reprogramming may be used to generate therapeutically applicable iPSCs. PMID:19337237

  10. Herpesvirus mutagenesis facilitated by infectious bacterial artificial chromosomes (iBACs).

    PubMed

    Robinson, Karl E; Mahony, Timothy J

    2015-01-01

    A critical factor in the study of herpesviruses, their genes and gene functions is the capacity to derive mutants that harbor deletions, truncations, or insertions within the genetic elements of interest. Once constructed the impact of the introduced mutation on the phenotypic properties of the rescued virus can be determined in either in vitro or in vivo systems. However, the construction of such mutants by traditional virological mutagenesis techniques can be a difficult and laborious undertaking. The maintenance of a viral genome as an infectious bacterial artificial chromosome (iBAC), however, endows the capacity to manipulate the viral genome for mutagenesis studies with relative ease. Here, the construction and characterization of two gene deletion mutants of an alphaherpesvirus maintained as iBAC in combination with an inducible homologous recombination system in Escherichia coli is detailed. The methodology is generally applicable to any iBAC and is demonstrated to be a highly efficient and informative approach for mutant virus construction. PMID:25239746

  11. Generation of an inducible and optimized piggyBac transposon system†

    PubMed Central

    Cadiñanos, Juan; Bradley, Allan

    2007-01-01

    Genomic studies in the mouse have been slowed by the lack of transposon-mediated mutagenesis. However, since the resurrection of Sleeping Beauty (SB), the possibility of performing forward genetics in mice has been reinforced. Recently, piggyBac (PB), a functional transposon from insects, was also described to work in mammals. As the activity of PB is higher than that of SB11 and SB12, two hyperactive SB transposases, we have characterized and improved the PB system in mouse ES cells. We have generated a mouse codon-optimized version of the PB transposase coding sequence (CDS) which provides transposition levels greater than the original. We have also found that the promoter sequence predicted in the 5′-terminal repeat of the PB transposon is active in the mammalian context. Finally, we have engineered inducible versions of the optimized piggyBac transposase fused with ERT2. One of them, when induced, provides higher levels of transposition than the native piggyBac CDS, whereas in the absence of induction its activity is indistinguishable from background. We expect that these tools, adaptable to perform mouse-germline mutagenesis, will facilitate the identification of genes involved in pathological and physiological processes, such as cancer or ES cell differentiation. PMID:17576687

  12. Enforcement following 0.08% BAC law change: sex-specific consequences of changing arrest practices?

    PubMed

    Schwartz, Jennifer; Davaran, Ardavan

    2013-10-01

    This research evaluated effects of stricter 0.08% BAC drunken driving law on changes in sex-specific DUI arrest rates, controlling for increased law enforcement resources and shifts in DUI-related behaviors. Another main purpose, the study assessed female/male differences in arrest increases due to broader enforcement standards and efforts. Panel data was assembled for 24 states over 1990-2007 on DUI arrests, alcohol policy, law enforcement resources, drinking and drunken driving prevalence. Two-way fixed-effects seemingly unrelated regression models predicted female versus male changes in DUI arrests following implementation of lower legal limits of intoxication, net controls. Findings suggest, first, that a broader legal definition of drunken driving intending to officially sanction less serious offenders (0.08% vs. 0.10% BAC) was associated with increased DUI arrests for both sexes. Second, growth in specialized DUI-enforcement units also was related to increased arrests. Whereas male and female arrest trends were equally affected by the direct net-widening effects of 0.08% BAC alcohol-policy, specialized DUI-enforcement efforts to dig deeper into the offender-pool had stronger arrest-producing effects on females, particularly prior to law change. Specifying how changes in law and enforcement resources affect arrest outcomes is an important pre-cursor to alcohol-policy analyses of effectiveness. A potential unintended consequence, effects of law and enforcement may differ across population segments. PMID:23773958

  13. Impact of BAC limit reduction on different population segments: a Poisson fixed effect analysis.

    PubMed

    Kaplan, Sigal; Prato, Carlo Giacomo

    2007-11-01

    Over the past few decades, several countries enacted the reduction of the legal blood alcohol concentration (BAC) limit, often alongside the administrative license revocation or suspension, to battle drinking-and-driving behavior. Several researchers investigated the effectiveness of these policies by applying different analysis procedures, while assuming population homogeneity in responding to these laws. The present analysis focuses on the evaluation of the impact of BAC limit reduction on different population segments. Poisson regression models, adapted to account for possible observation dependence over time and state specific effects, are estimated to measure the reduction of the number of alcohol-related accidents and fatalities for single-vehicle accidents in 22 U.S. jurisdictions over a period of 15 years starting in 1990. Model estimates demonstrate that, for alcohol-related single-vehicle crashes, (i) BAC laws are more effective in terms of reduction of number of casualties rather than number of accidents, (ii) women and elderly population exhibit higher law compliance with respect to men and to young adult and adult population, respectively, and (iii) the presence of passengers in the vehicle enhances the sense of responsibility of the driver. PMID:17920837

  14. Combined BAC and MIEX pre-treatment of secondary wastewater effluent to reduce fouling of nanofiltration membranes.

    PubMed

    Aryal, Ashok; Sathasivan, Arumugam; Heitz, Anna; Zheng, Gang; Nikraz, Hamid; Ginige, Maneesha P

    2015-03-01

    Biological activated carbon (BAC) and magnetic ion exchange resin (MIEX) were used to pre-treat secondary wastewater effluent (SWWE) and assessed for their capacity to reduce fouling of a nanofiltration membrane. BAC pre-treated water facilitated a lower but a steady flux while MIEX treated water resulted in a higher but a rapidly declining flux. Their combined use increased average flux from 58 to 89%. MIEX combined with BAC, in that order, was superior in reducing membrane fouling. Measurement of average Stokes radius (m) and apparent molecular weight distribution of dissolved organic matter (DOM), by nuclear magnetic resonance (NMR) and liquid chromatography organic carbon detection (LC-OCD), respectively, revealed that the microbial activity of BAC changed the nature of organic matter, probably by increasing the size of DOM molecules. BAC generally decreased the lower apparent molecular weight (LMW) fraction of dissolved organic carbon (DOC). Hence, the removal of LMW DOC and an increase of average Stokes radius (m) of DOM appeared to be important in facilitating a longer steady flux. Specifically, the combined MIEX/BAC pre-treatments appeared to target and reduce the foulants in SWWE that are largely responsible for the reduction of flux in nanofiltration membranes. PMID:25540835

  15. Libraries, Ebooks, and Competition

    ERIC Educational Resources Information Center

    Hellman, Eric

    2010-01-01

    People keep writing articles about how valuable libraries are, even with ebooks and the Internet. What people are overlooking is that the reason libraries are having such fits dealing with a changing environment is not that libraries are unrecognized as fountains of value, it's that libraries are so valuable that they attract voracious new…

  16. The Library Building Tomorrow.

    ERIC Educational Resources Information Center

    Waters, Richard L.

    1987-01-01

    Examination of the library of tomorrow speculates about the impact of changes in the functions of government, technology, demographics, lifestyle, and values on the role of the library. A facility for the contemporary public library is described that can both accommodate traditional services and respond to changes in the library's role. (17…

  17. School Libraries in Hawaii.

    ERIC Educational Resources Information Center

    Bard, Therese Bissen

    This paper outlines the history, functions, administration, and current focus of school library services in Hawaii, which is the only state in the United States with a library staffed by a trained librarian in every public school. Its first school library was established in 1882. Elementary school libraries developed concurrently with secondary…

  18. California: Library Information Technologies.

    ERIC Educational Resources Information Center

    Will, Barbara, Ed.

    1996-01-01

    Describes six information technology projects in California libraries, including Internet access in public libraries; digital library developments at the University of California, Berkeley; the World Wide Web home page for the state library; Pacific Bell's role in statewide connectivity; state government initiatives; and services of the state…

  19. Economics of Academic Libraries.

    ERIC Educational Resources Information Center

    Baumol, William J.; Marcus, Matityahu

    An analysis is conducted of economic issues pertinent to library planning in higher education in the face of rising costs and diminishing financial support. The individual chapters deal with: 1) growth rates in large university libraries; 2) library costs in colleges and universities; 3) cost trends and long-range plans; 4) library data; and 5) a…

  20. Alaska Library Directory, 1996.

    ERIC Educational Resources Information Center

    Jennings, Mary, Ed.

    This directory of Alaska's Libraries lists: members of the Alaska Library Association (AkLA) Executive Council and Committee Chairs; State Board of Education members; members of the Governor's Advisory Council on Libraries; school, academic and public libraries and their addresses, phone and fax numbers, and contact persons; personal,…

  1. Growing Competition for Libraries.

    ERIC Educational Resources Information Center

    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…

  2. The New Library Professional

    ERIC Educational Resources Information Center

    Wilder, Stanley

    2007-01-01

    This article discusses what the growing generation gap among library employees mean for academic research libraries and for the profession. Viewed collectively, the members of the under-35 cohort are a harbinger of a new kind of academic library professional, one whose traits bear directly on the ability of libraries to thrive amid the continuing…

  3. AMERICA 2000 Library Partnership.

    ERIC Educational Resources Information Center

    Office of Educational Research and Improvement (ED), Washington, DC.

    The United States Department of Education, the National Endowment for the Humanities, the Library of Congress, the National Commission on Libraries and Information Science, and the National Institute for Literacy have formed the AMERICA 2000 Library Partnership to support libraries in their work toward the six National Education Goals announced by…

  4. Conservation of Library Materials.

    ERIC Educational Resources Information Center

    Illinois Libraries, 1985

    1985-01-01

    Twelve articles cover books as artifacts; workstations for conservation of library materials; care of scrapbooks, albums, and photographs; map preservation; library environment; flood recovery; disaster prevention and preparedness; incorporating preservation into library organization; and bibliography of Chester Public Library (Illinois) First…

  5. The Bush Memorial Library.

    ERIC Educational Resources Information Center

    Hamline University Bulletin, 1971

    1971-01-01

    The Bush Memorial Library was formally dedicated on October 9, 1971. As part of Hamline University in St. Paul, Minnesota, the Bush Memorial Library has a reading room, audio booths, and audio-visual classroom as well as an audio control room. The Bush Memorial Library is a member of the Cooperating Libraries in Consortium which is a cooperative…

  6. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.

    PubMed

    Muñoz-Amatriaín, María; Lonardi, Stefano; Luo, MingCheng; Madishetty, Kavitha; Svensson, Jan T; Moscou, Matthew J; Wanamaker, Steve; Jiang, Tao; Kleinhofs, Andris; Muehlbauer, Gary J; Wise, Roger P; Stein, Nils; Ma, Yaqin; Rodriguez, Edmundo; Kudrna, Dave; Bhat, Prasanna R; Chao, Shiaoman; Condamine, Pascal; Heinen, Shane; Resnik, Josh; Wing, Rod; Witt, Heather N; Alpert, Matthew; Beccuti, Marco; Bozdag, Serdar; Cordero, Francesca; Mirebrahim, Hamid; Ounit, Rachid; Wu, Yonghui; You, Frank; Zheng, Jie; Simková, Hana; Dolezel, Jaroslav; Grimwood, Jane; Schmutz, Jeremy; Duma, Denisa; Altschmied, Lothar; Blake, Tom; Bregitzer, Phil; Cooper, Laurel; Dilbirligi, Muharrem; Falk, Anders; Feiz, Leila; Graner, Andreas; Gustafson, Perry; Hayes, Patrick M; Lemaux, Peggy; Mammadov, Jafar; Close, Timothy J

    2015-10-01

    Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant. PMID:26252423

  7. 23 CFR Appendix A to Part 1225 - Effects of the 0.08 BAC Sanction Program on Non-Complying States

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Effects of the 0.08 BAC Sanction Program on Non... INTOXICATED PERSONS Pt. 1225, App. A Appendix A to Part 1225—Effects of the 0.08 BAC Sanction Program on Non-Complying States Effects of the 0.08 BAC Sanction Program on Non-Complying States Fiscalyear Withhold...

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

    ERIC Educational Resources Information Center

    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…

  9. Computational analysis of ordering in higher homologous series of nBAC: The effect of a dielectric medium

    SciTech Connect

    Ojha, D. P.

    2006-12-15

    A computational analysis of ordering in higher homologous series of p-n-alkylbenzoic acids (nBAC) that have 7 (7BAC) and 9 (9BAC) carbon atoms in the alkyl chain has been carried out on the basis of quantum mechanics and intermolecular forces. The molecular geometry of 7BAC and 9BAC has been constructed on the basis of published crystallographic data with the standard values of bond lengths and bond angles. The evaluation of atomic charge and dipole moment at each atomic center has been carried out through the complete neglect differential overlap (CNDO/2) method. The configurational energy has been computed via the Rayleigh-Schroedinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration in a dielectric medium at the nematic-isotropic-transition temperature through the use of the Maxwell-Boltzmann formula. It has been observed that there is a considerable rise in the probability of interactions, although the order of preference remains the same. The present article offers theoretical support to the experimental observations. In addition, this provides a new way of looking at the liquid-crystalline molecules in a dielectric medium.

  10. Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.

    PubMed

    Seefeldt, A Carolin; Graf, Michael; Pérébaskine, Natacha; Nguyen, Fabian; Arenz, Stefan; Mardirossian, Mario; Scocchi, Marco; Wilson, Daniel N; Innis, C Axel

    2016-03-18

    Proline-rich antimicrobial peptides (PrAMPs) produced as part of the innate immune response of animals, insects and plants represent a vast, untapped resource for the treatment of multidrug-resistant bacterial infections. PrAMPs such as oncocin or bactenecin-7 (Bac7) interact with the bacterial ribosome to inhibit translation, but their supposed specificity as inhibitors of bacterial rather than mammalian protein synthesis remains unclear, despite being key to developing drugs with low toxicity. Here, we present crystal structures of the Thermus thermophilus 70S ribosome in complex with the first 16 residues of mammalian Bac7, as well as the insect-derived PrAMPs metalnikowin I and pyrrhocoricin. The structures reveal that the mammalian Bac7 interacts with a similar region of the ribosome as insect-derived PrAMPs. Consistently, Bac7 and the oncocin derivative Onc112 compete effectively with antibiotics, such as erythromycin, which target the ribosomal exit tunnel. Moreover, we demonstrate that Bac7 allows initiation complex formation but prevents entry into the elongation phase of translation, and show that it inhibits translation on both mammalian and bacterial ribosomes, explaining why this peptide needs to be stored as an inactive pro-peptide. These findings highlight the need to consider the specificity of PrAMP derivatives for the bacterial ribosome in future drug development efforts. PMID:26792896

  11. Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis.

    PubMed

    Hofemeister, Helmut; Ciotta, Giovanni; Fu, Jun; Seibert, Philipp Martin; Schulz, Alexander; Maresca, Marcello; Sarov, Mihail; Anastassiadis, Konstantinos; Stewart, A Francis

    2011-04-01

    Protein tagging offers many advantages for proteomic and regulomic research. Ideally, protein tagging is equivalent to having a high affinity antibody for every chosen protein. However, these advantages are compromised if the tagged protein is overexpressed, which is usually the case from cDNA expression vectors. Physiological expression of tagged proteins can be achieved by gene targeting to knock-in the protein tag or by BAC transgenesis. BAC transgenes usually retain the native gene architecture including all cis-regulatory elements as well as the exon-intron configurations. Consequently most BAC transgenes are authentically regulated (e.g. by transcription factors, cell cycle, miRNA) and can be alternatively spliced. Recombineering has become the method of choice for generating targeting constructs or modifying BACs. Here we present methods with detailed protocols for protein tagging by recombineering for BAC transgenesis and/or gene targeting, including the evaluation of tagged protein expression, the retrieval of associated protein complexes for mass spectrometry and the use of the tags in ChIP (chromatin immunoprecipitation). PMID:21195765

  12. Purification and partial characterization of a novel antibacterial agent (Bac1829) Produced by Staphylococcus aureus KSI1829.

    PubMed Central

    Crupper, S S; Iandolo, J J

    1996-01-01

    A novel antimicrobial agent from Staphylococcus aureus KSI1829, designated Bac1829, was purified by sequential steps of ammonium sulfate precipitation, Sephadex G-50 gel filtration chromatography, and hydrophobic interaction chromatography. Purified Bac1829 has a molecular mass of 6,418 +/- 2 Da. The peptide in heat stable, since full biological activity is retained after heating at 95 degrees C for 15 min, and it is destroyed by digestion with proteases. Amino acid sequence analysis revealed a high concentration of Ala and Gly residues, which respectively comprised 24 and 19% of the total amino acid content. Additionally, high levels of hydrophobic amino acids were present, accounting for the hydrophobic nature of Bac1829. Purified Bac1829 killed exponentially growing Corynebacterium renale in a dose-dependent manner by a bactericidal mode of action. A partial inhibitory spectrum analysis revealed that the following organisms were sensitive to the inhibitory activity of Bac1829: S. aureus RN4220, Streptococcus suis, Corynebacterium pseudotuberculosis, C. renale, Corynebacterium diptheriae, Haemophilus parasuis, Bordetella pertussis, Bordetella bronchoseptica, Moraxella bovis, and Pasteurella multocida. PMID:8795206

  13. The first generation of a BAC-based physical map of Brassica rapa

    PubMed Central

    Mun, Jeong-Hwan; Kwon, Soo-Jin; Yang, Tae-Jin; Kim, Hye-Sun; Choi, Beom-Soon; Baek, Seunghoon; Kim, Jung Sun; Jin, Mina; Kim, Jin A; Lim, Myung-Ho; Lee, Soo In; Kim, Ho-Il; Kim, Hyungtae; Lim, Yong Pyo; Park, Beom-Seok

    2008-01-01

    Background The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. Results A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. Conclusion The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community. PMID:18549474

  14. Reprogramming of mouse amniotic fluid cells using a PiggyBac transposon system.

    PubMed

    Bertin, E; Piccoli, M; Franzin, C; Nagy, A; Mileikovsky, M; De Coppi, P; Pozzobon, M

    2015-11-01

    Induced pluripotent stem (iPS) cells are generated from mouse and human somatic cells by forced expression of defined transcription factors using different methods. Amniotic fluid (AF) cells are easy to obtain from routinely scheduled procedures for prenatal diagnosis and iPS cells have been generated from human AF. Here, we generated iPS cells from mouse AF cells, using a non-viral-based approach constituted by the PiggyBac (PB) transposon system. All iPS cell lines obtained exhibited characteristics of pluripotent cells, including the ability to differentiate toward derivatives of all three germ layers in vitro and in vivo. PMID:26987920

  15. Optimization of WDM lightwave systems (BAC) design using error control coding

    NASA Astrophysics Data System (ADS)

    Mruthyunjaya, H. S.; Umesh, G.; Sathish Kumar, M.

    2007-04-01

    In a binary asymmetric channel (BAC) it may be necessary to correct only those errors which result from incorrect transmission of one of the two code elements. In optical fiber multichannel systems, the optical amplifiers are critical components and amplified spontaneous emission noise in the optical amplifiers is the major source of noise in it. The property of erbium doped fiber amplifier is nearly ideal for application in lightwave long haul transmission. We investigate performance of error correcting codes in such systems in presence of stimulated Raman scattering and amplified spontaneous emission noise with asymmetric channel statistics. Performance of some best known concatenated coding schemes is reported.

  16. Hyperactive self-inactivating piggyBac for transposase-enhanced pronuclear microinjection transgenesis.

    PubMed

    Marh, Joel; Stoytcheva, Zoia; Urschitz, Johann; Sugawara, Atsushi; Yamashiro, Hideaki; Owens, Jesse B; Stoytchev, Ilko; Pelczar, Pawel; Yanagimachi, Ryuzo; Moisyadi, Stefan

    2012-11-20

    We have developed a unique method for mouse transgenesis. The transposase-enhanced pronuclear microinjection (PNI) technique described herein uses the hyperactive piggyBac transposase to insert a large transgene into the mouse genome. This procedure increased transgene integration efficiency by fivefold compared with conventional PNI or intracytoplasmic sperm injection-mediated transgenesis. Our data indicate that the transposase-enhanced PNI technique additionally requires fewer embryos to be microinjected than traditional methods to obtain transgenic animals. This transposase-mediated approach is also very efficient for single-cell embryo cytoplasmic injections, offering an easy-to-implement transgenesis method to the scientific community. PMID:23093669

  17. Germline transformation of Aedes fluviatilis (Diptera:Culicidae) with the piggyBac transposable element.

    PubMed

    Rodrigues, Flávia Guimarães; Oliveira, Sabrina Barbosa; Rocha, Bruno Coelho; Moreira, Luciano Andrade

    2006-11-01

    The technique to generate transgenic mosquitoes requires adaptation for each target species because of aspects related to species biology, sensitivity to manipulation and rearing conditions. Here we tested different parameters on the microinjection procedure in order to obtain a transgenic Neotropical mosquito species. By using a transposon-based strategy we were able to successfully transform Aedes fluviatilis (Lutz), which can be used as an avian malaria model. These results demonstrate the usefulness of the piggyBac transposable element as a transformation vector for Neotropical mosquito species and opens up new research frontiers for South American mosquito vectors. PMID:17160283

  18. Art Libraries Section. Special Libraries Division. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    Papers on art libraries and information services for the arts, which were presented at the 1983 International Federation of Library Associations (IFLA) conference, include: (1) "'I See All': Information Technology and the Universal Availability of Images" by Philip Pacey (United Kingdom); (2) "Online Databases in the Fine Arts" by Michael Rinehart…

  19. Comparison of the MB/BacT System with a Revised Antibiotic Supplement Kit to the BACTEC 460 System for Detection of Mycobacteria in Clinical Specimens

    PubMed Central

    Benjamin, W. H.; Waites, K. B.; Beverly, A.; Gibbs, L.; Waller, M.; Nix, S.; Moser, S. A.; Willert, M.

    1998-01-01

    The MB/BacT system (MB/BacT) with a revised antibiotic supplement kit was compared with the BACTEC 460 system (BACTEC 460) in a test of 488 specimens submitted for mycobacterial culture from 302 patients. Twenty-four Mycobacterium tuberculosis isolates were detected by the BACTEC 460 versus 23 isolates by the MB/BacT. Mean time until detection of M. tuberculosis isolates identified by both systems was 11.9 days for the BACTEC 460 versus 13.7 days for the MB/BacT (P = 0.046). M. avium complex was detected in 12 specimens by the MB/BacT versus 10 specimens by the BACTEC 460. Only 8 of 14 (57%) M. avium isolates were detected by both systems, with a mean time until detection of 10.1 days for the BACTEC 460 and 14.2 days for the MB/BacT (P = 0.009). The BACTEC 460 and the MB/BacT detected M. gordonae in four specimens, but only a single specimen was positive by both systems. One M. fortuitum isolate and one of five M. kansasii isolates were recovered only by the BACTEC 460. The bacterial overgrowth rate was 7.0% for the MB/BacT versus 4.1% for the BACTEC 460. We found the MB/BacT to be comparable to the BACTEC 460 for mycobacterial detection. Even though time until detection with the MB/BacT was slightly longer (1.8 days longer for M. tuberculosis and 4.1 days for M. avium [mean values]) and the bacterial overgrowth rate was somewhat higher, the decreased labor, the availability of a computerized data management system, and the noninvasive, nonradiometric aspects of the MB/BacT offset these relative disadvantages and make it an acceptable alternative for use in the diagnostic laboratory. PMID:9774571

  20. A Genetic Screen Using the PiggyBac Transposon in Haploid Cells Identifies Parp1 as a Mediator of Olaparib Toxicity

    PubMed Central

    Pettitt, Stephen J.; Rehman, Farah L.; Bajrami, Ilirjana; Brough, Rachel; Wallberg, Fredrik; Kozarewa, Iwanka; Fenwick, Kerry; Assiotis, Ioannis; Chen, Lina; Campbell, James; Lord, Christopher J.; Ashworth, Alan

    2013-01-01

    Genetic perturbation screens have the potential to dissect a wide range of cellular phenotypes. Such screens have historically been difficult in diploid mammalian cells. The recent derivation of haploid embryonic stem cells provides an opportunity to cause loss of function mutants with a random mutagen in a mammalian cell with a normal genetic background. We describe an approach to genetic screens that exploits the highly active piggyBac transposon in haploid mammalian cells. As an example of haploid transposon (HTP) screening, we apply this approach to identifying determinants of cancer drug toxicity and resistance. In a screen for 6-thioguanine resistance we recovered components of the DNA mismatch repair pathway, a known requirement for toxicity. In a further screen for resistance to the clinical poly(ADP-ribose) polymerase (PARP) inhibitor olaparib we recovered multiple Parp1 mutants. Our results show that olaparib toxicity to normal cells is mediated predominantly via Parp1, and suggest that the clinical side effects of olaparib may be on target. The transposon mutant libraries are stable and can be readily reused to screen other drugs. The screening protocol described has several advantages over other methods such as RNA interference: it is rapid and low cost, and mutations can be easily reverted to establish causality. PMID:23634208

  1. The Libraries of Rio.

    ERIC Educational Resources Information Center

    Foster, Barbara

    1988-01-01

    Describes aspects of several libraries in Rio de Janeiro. Topics covered include library policies, budgets, periodicals and books in the collections, classification schemes used, and literary areas of interest to patrons. (6 references) (CLB)

  2. Facility Focus: Libraries.

    ERIC Educational Resources Information Center

    College Planning & Management, 2003

    2003-01-01

    Describes the designs of the Ferris State University Library for Information, Technology and Education (FLITE), and the Meyer Library and Information Technology Center at Southwest Missouri State University. Includes photographs. (EV)

  3. Selecting Library Furniture & Equipment.

    ERIC Educational Resources Information Center

    Media & Methods, 1997

    1997-01-01

    Offers suggestions for selecting school library furniture and equipment. Describes various models of computer workstations; reading tables and chairs; and shelving. Sidebar lists names and addresses of library furniture manufactures and distributors. (AEF)

  4. Medical Library Association

    MedlinePlus

    ... 11th, 2016 Patricia Flatley Brennan, registered nurse, informatician, industrial engineer, and renowned researcher is appointed as Director of the National Library of Medicine Tweets Copyright © 2016 Medical Library Association. ...

  5. Israeli Special Libraries

    ERIC Educational Resources Information Center

    Foster, Barbara

    1974-01-01

    Israel is sprinkled with a noteworthy representation of special libraries which run the gamut from modest kibbutz efforts to highly technical scientific and humanities libraries. A few examples are discussed here. (Author/CH)

  6. Characteristics of Highly Polymorphic Segmental Copy-Number Variations Observed in Japanese by BAC-Array-CGH

    PubMed Central

    Takahashi, Norio; Satoh, Yasunari; Sasaki, Keiko; Shimoichi, Yuko; Sugita, Keiko; Katayama, Hiroaki

    2011-01-01

    Segmental copy-number variations (CNVs) may contribute to genetic variation in humans. Reports of the existence and characteristics of CNVs in a large Japanese cohort are quite limited. We report the data from a large Japanese population. We conducted population screening for 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC-aCGH). We summarize the data by focusing on highly polymorphic CNVs in ≥5.0% of the individual, since they may be informative for demonstrating the relationships between genotypes and their phenotypes. We found a total of 680 CNVs at 16 different BAC-regions in the genome. The majority of the polymorphic CNVs presented on BAC-clones that overlapped with regions of segmental duplication, and the majority of the polymorphic CNVs observed in this population had been previously reported in other publications. Some of the CNVs contained genes which might be related to phenotypic heterogeneity among individuals. PMID:21197411

  7. Physicochemical Studies on Orientation and Conformation of a New Bacteriocin BacSp222 in a Planar Phospholipid Bilayer.

    PubMed

    Pieta, Piotr; Majewska, Marta; Su, Zhangfei; Grossutti, Michael; Wladyka, Benedykt; Piejko, Marcin; Lipkowski, Jacek; Mak, Pawel

    2016-06-01

    The behavior, secondary structure, and orientation of a recently discovered bacteriocin-like peptide BacSp222 in a lipid model system supported at a gold electrode was investigated by chronocoulometry, polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and attenuated total reflectance infrared (ATR-IR) spectroscopy. The IR spectra show that the secondary structure of BacSp222 is predominantly α-helical. Analysis of the spectra in the amide I region shows that the α-helical fragment of the peptide is inserted into bilayer at the potential range at which the bilayer is stable and attached to the Au(111) surface, i.e., from -0.5 to 0.3 V vs Ag/AgCl. Insertion of BacSp222 to the membrane significantly changes the conformation of the acyl chains of lipid molecules, from all-trans to partially melted; however, the chains become less tilted. Based on these results, we propose that BacSp222 interacts with the DMPC bilayer through the barrel-stave pore formation. In this model, α-helix of BacSp222 inserts into the membrane with an angle between the α-helix axis and membrane normal equal to ∼18°. The changes in orientation of the α-helical fragment of the peptide indicate that the orientation of BacSp222 with respect to the bilayer surface is potential-dependent. The peptide is inserted into the membrane driven by the electrostatic field generated by negative charge at the metal surface. It is not inserted at negative potentials where the membrane is detached from the metal and no longer exposed to the electrostatic field of the metal. PMID:27124645

  8. Bookmarking Your Library's Teens.

    ERIC Educational Resources Information Center

    Williams, Mary Pasek

    1999-01-01

    Describes one public library's project of photographing teenagers reading around the library and making the photos into bookmarks with the library logo and a "read" message. Discusses the background, arrangements, photo session, assembly, distribution and publicity, and funding and community response. (AEF)

  9. The End of Libraries.

    ERIC Educational Resources Information Center

    Thompson, James

    1983-01-01

    Suggests that if librarians and libraries are to continue to fulfill their true tasks, they need to adapt to changes resulting from new technology and overcome the professional paralysis that has made most major libraries largely unusable. Problems of size, arrangement, and catalogs are identified as contributors to unusable library. (EJS)

  10. Library Studies I Workbook.

    ERIC Educational Resources Information Center

    Frost, William J.

    Developed for use in the Library Studies I component of the Library Studies Program at Bloomsburg University (Pennsylvania), this self-paced workbook is intended to acquaint students with the Harvey A. Andruss Library and help them develop information-seeking skills. The workbook is designed to be used in conjunction with an exercise book, and…

  11. Art for Libraries' Sake.

    ERIC Educational Resources Information Center

    Lugo, Mark-Elliot

    1999-01-01

    Illustrates the benefits of an aggressive library program of regularly scheduled and professionally curated art exhibitions and related events. Describes the Visual Arts Program at the Pacific Beach branch library (San Diego). A sidebar by Debra Wilcox Johnson discusses libraries' development of cultural programming for adults. (AEF)

  12. California Library Laws, 2009

    ERIC Educational Resources Information Center

    Smith, Paul G., Ed.

    2009-01-01

    California Library Laws 2009 is a selective guide to state laws and related materials that most directly affect the everyday operations of public libraries and organizations that work with public libraries. It is intended as a convenient reference, not as a replacement for the annotated codes or for legal advice. The guide is organized as follows.…

  13. California Library Laws, 2008

    ERIC Educational Resources Information Center

    Smith, Paul G., Ed.

    2008-01-01

    "California Library Laws 2008" is a selective guide to state laws and related materials that most directly affect the everyday operations of public libraries and organizations that work with public libraries. It is intended as a convenient reference, not as a replacement for the annotated codes or for legal advice. The guide is organized as…

  14. A Library That Swings

    ERIC Educational Resources Information Center

    Spragens, Thomas A.

    1971-01-01

    The Grace Doherty Library (Centre College, Danville, Kentucky) is a library that "swings," being so designed that a substantial part of its space is used alternately for classroom purposes during the day and for library reading-study space in the peak evening hours. (Author)

  15. School Libraries in Fiji.

    ERIC Educational Resources Information Center

    Singh, Harry

    1995-01-01

    Presents a 50-year history of school library development and national educational programs in Fiji and discusses the future of Fiji's elementary and secondary school libraries. Examines obstacles to school library development including government ignorance, lack of trained librarians, changes in school curriculum, lack of financing, and high costs…

  16. Marketing Academic Libraries

    ERIC Educational Resources Information Center

    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. The Toy Lending Library.

    ERIC Educational Resources Information Center

    Wiscont, Jeanne Mull

    This paper explores the concept of toy lending libraries. The first six chapters discuss: (1) the history of toy lending libraries; (2) the values and purposes of using games and toys with children; (2) the contribution of games and toys to the goals of a children's services library division; (3) examples of toy lending service in public…

  18. The Library Morphs

    ERIC Educational Resources Information Center

    Waters, John K.

    2008-01-01

    As campus renovation projects go, the Ohio State University's plan to turn its main library into "a library for the 21st century" is ambitious. The author describes the decade-long, $109 million transformation of the William Oxley Thompson Memorial Library. The overhaul calls for a complete replacement of all mechanical and electrical systems,…

  19. A Truly Bookless Library

    ERIC Educational Resources Information Center

    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…

  20. Simple Library Bookkeeping.

    ERIC Educational Resources Information Center

    Hoffman, Herbert H.

    A simple and cheap manual double entry continuous transaction posting system with running balances is developed for bookkeeping by small libraries. A very small library may operate without any system of fiscal control but when a library's budget approaches three figures, some kind of bookkeeping must be introduced. To maintain control over his…

  1. Library Awareness Survey.

    ERIC Educational Resources Information Center

    Rice, James

    1992-01-01

    Reports results of a survey of Iowa City residents regarding their awareness of public library services. Data are presented on use of the library for factual information, statistical/numerical information, learning, and information not available at home; awareness of in-person and telephone library reference services; and knowledge about…

  2. PAL: Positional Astronomy Library

    NASA Astrophysics Data System (ADS)

    Jenness, T.; Berry, D. S.

    2016-06-01

    The PAL library is a partial re-implementation of Pat Wallace's popular SLALIB library written in C using a Gnu GPL license and layered on top of the IAU's SOFA library (or the BSD-licensed ERFA) where appropriate. PAL attempts to stick to the SLA C API where possible.

  3. Environmental Library Systems

    ERIC Educational Resources Information Center

    Thomas, Sarah M.; Needle, Lester P.

    1975-01-01

    The U. S. Environmental Protection Agency (EPA) Library System consists of 28 libraries. The libraries are supported by computer systems covering journal and book holdings, journal check-in, circulation, document control, EPA reports, international exchange items, and specialized subject area collections. (Author)

  4. Worthington Libraries, OH

    ERIC Educational Resources Information Center

    Berry, John N., III

    2007-01-01

    Worthington, Ohio, has deep library roots. A library has been part of its history since the planning by settlers before the city's birth in 1803. Among the treasures brought by James Kilbourne and the Scioto Company from Connecticut to the new, planned community they built was a collection of books for their new subscription library. The books…

  5. Staffing the College Library

    ERIC Educational Resources Information Center

    Thomas, Bruce

    1973-01-01

    College libraries use a variety of methods to identify and select professional library personnel. 70 libraries responded to a questionnaire about their methods and the results are presented. The effectiveness of advertisements, employment services, testing and reference checks are among the topics discussed. (DH)

  6. Merchandising Your Library.

    ERIC Educational Resources Information Center

    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…

  7. Libraries and the Environment.

    ERIC Educational Resources Information Center

    LaRue, James; And Others

    1991-01-01

    Three articles address issues that relate to libraries and the environment. Highlights include recycling projects; buying recycled paper products and other ecology-minded purchasing ideas; energy-efficient libraries; indoor pollution problems; a list of environmental information sources; designing library buildings; and activities that libraries…

  8. The Honor System Library

    ERIC Educational Resources Information Center

    Marie, Kristen L.

    2005-01-01

    An honor system library can be created inside the library media center (LMC). Where students can access free books and magazines that require no formal checkouts. The honor library system at Washington High School, Fremont, California, has become self-sustaining. As many students, parents and teachers donate quality material. No student is ever…

  9. School Libraries and Innovation

    ERIC Educational Resources Information Center

    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. Changing State Digital Libraries

    ERIC Educational Resources Information Center

    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…

  11. The Michigan Electronic Library.

    ERIC Educational Resources Information Center

    Davidsen, Susanna L.

    1997-01-01

    Describes the Michigan Electronic Library (MEL), the largest evaluated and organized Web-based library of Internet resources, that was designed to provide a library of electronic information resources selected by librarians. MEL's partnership is explained, the collection is described, and future developments are considered. (LRW)

  12. Summer Library Reading Programs

    ERIC Educational Resources Information Center

    Fiore, Carole D.

    2007-01-01

    Virtually all public libraries in the United States provide some type of summer library reading program during the traditional summer vacation period. Summer library reading programs provide opportunities for students of many ages and abilities to practice their reading skills and maintain skills that are developed during the school year. Fiore…

  13. Spanish Museum Libraries Network.

    ERIC Educational Resources Information Center

    Lopez de Prado, Rosario

    This paper describes the creation of an automated network of museum libraries in Spain. The only way in which the specialized libraries in the world today can continue to be active and to offer valid information is to automate the service they offer, and create network libraries with cooperative plans. The network can be configured with different…

  14. International School Library Day.

    ERIC Educational Resources Information Center

    Clyde, Laurel A.

    2001-01-01

    Describes the development of an International School Library Day and discusses activities in Australian school libraries. Highlights include the development of Web pages; sponsorship by national, state, or provincial associations; publicity materials; joint activities with other countries; student involvement; and activities with public libraries.…

  15. Technostress and Library Values.

    ERIC Educational Resources Information Center

    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)

  16. Supervision in Libraries.

    ERIC Educational Resources Information Center

    Bailey, Martha J.

    Although the literature of library administration draws extensively on that of business management, it is difficult to compare library supervision to business or industrial supervision. Library supervisors often do not have managerial training and may consider their management role as secondary. The educational level of the staff they supervise…

  17. Public Libraries Going Green

    ERIC Educational Resources Information Center

    Miller, Kathryn

    2010-01-01

    Going green is now a national issue, and patrons expect their library to respond in the same way many corporations have. Libraries are going green with logos on their Web sites, programs for the public, and a host of other initiatives. This is the first book to focus strictly on the library's role in going green, helping you with: (1) Collection…

  18. Automation in Libraries.

    ERIC Educational Resources Information Center

    Canadian Library Association, Ottawa (Ontario).

    The fourth Canadian Association of College and University Libraries (CACUL) Conference on Library Automation was held in Hamilton, June 20-21, 1970, as a pre-conference workshop of the Canadian Library Association (CLA). The purpose of the conference was to present papers on current projects and to discuss the continuing need for this type of…

  19. Libraries in Africa.

    ERIC Educational Resources Information Center

    Enyia, Christian O.; And Others

    1991-01-01

    Includes five articles that discuss library and information work in Africa. Highlights include computerization in Nigerian libraries; education for library and information services in Ghana; an evaluation of African librarianship; the role of Nigerian publishers in national development; and the role of information services in national development…

  20. An innovative process to improve turbidity and Organics Removal by BAC filters

    NASA Astrophysics Data System (ADS)

    Miao, Jia; Zhao, Qingliang; Wang, Baozhen; Li, Ji; Zhang, Jinsong

    2006-10-01

    The turbidity criterion for the product water of a WTP according to the State Project ‘863’ on the safeguard technology of drinking water in the southern areas of China is 0.1 NTU. The turbidity removal in the activated carbon filter was analyzed in a pilot-scale test and an innovative technology to improve the turbidity removal in a biologically activated carbon (BAC) filter was put forward in order to meet the criterion. Experimental results showed that the enhanced filtration by adding polymerized aluminium chloride (PAC) into the BAC filter was quite effective in turbidity control. The effluent turbidity was kept at a stable level (mean) of 0.033 NTU with a high removal of about 80% for influent turbidity of 0.110 0240 NTU with an addition of PAC at 0.05 mg L-1, meeting the requirement for filtrate turbidity equal to or less than 0.1 NTUC totally. In addition, the larger the PAC dosage was, the lower the effluent turbidity was. However, further improvement of turbidity removal was not obvious for PAC dosages beyond 0.l0 mg L-, and an optimal PAC dosage in the range of 0.05 0.10 mg L- was proposed.

  1. MBBR evaluation for oil refinery wastewater treatment, with post-ozonation and BAC, for wastewater reuse.

    PubMed

    Schneider, E E; Cerqueira, A C F P; Dezotti, M

    2011-01-01

    This work evaluated the performance of a Moving Bed Biofilm Reactor (MBBR) in the treatment of an oil refinery wastewater. Also, it investigated the possibility of reuse of the MBBR effluent, after ozonation in series with a biological activated carbon (BAC) column. The best performance of the MBBR was achieved with a hydraulic retention time (HRT) of 6 hours, employing a bed to bioreactor volume ratio (V(B)/V(R)) of 0.6. COD and N-NH₄(+) MBBR effluent concentrations ranged from 40 to 75 mg L⁻¹ (removal efficiency of 69-89%) and 2 to 6 mg L⁻¹ (removal efficiency of 45-86%), respectively. Ozonation carried out for 15 min with an ozone concentration of 5 mg L⁻¹ was able to improve the treated wastewater biodegradability. The treatment performance of the BAC columns was practically the same for ozonated and non ozonated MBBR effluents. The dissolved organic carbon (DOC) content of the columns of the activated carbon columns (CAG) was in the range of 2.1-3.8 mg L⁻¹, and the corresponding DOC removal efficiencies were comprised between 52 and 75%. The effluent obtained at the end of the proposed treatment presented a quality, which meet the requirements for water reuse in the oil refinery. PMID:21245566

  2. BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins

    PubMed Central

    Selvaraj, MuthuKrishnan; Puri, Munish; Dikshit, Kanak L.; Lefevre, Christophe

    2016-01-01

    The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL) proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Support vector machine (SVM) models were developed for predicting HbL proteins based upon amino acid composition (AC), dipeptide composition (DC), hybrid method (AC + DC), and position specific scoring matrix (PSSM). In addition, we introduce for the first time a new prediction method based on max to min amino acid residue (MM) profiles. The average accuracy, standard deviation (SD), false positive rate (FPR), confusion matrix, and receiver operating characteristic (ROC) were analyzed. We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques. Prediction accuracy was further investigated through confusion matrix and ROC curve analysis. All experimental results indicate that the proposed BacHbpred can be a perspective predictor for determination of HbL related proteins. BacHbpred, a web tool, has been developed for HbL prediction. PMID:27034664

  3. Hyperactive PiggyBac Transposons for Sustained and Robust Liver-targeted Gene Therapy

    PubMed Central

    Di Matteo, Mario; Samara-Kuko, Emira; Ward, Natalie J; Waddingon, Simon N; McVey, John H; Chuah, Marinee KL; VandenDriessche, Thierry

    2014-01-01

    The development of robust nonviral vectors could facilitate clinical gene therapy applications and may overcome some of the immune complications of viral vectors. Nevertheless, most nonviral gene deliver approaches typically yield only transient and/or low gene expression. To address these caveats, we have explored piggyBac transposons to correct hemophilia B by liver-directed factor IX (FIX) gene therapy in hemophilic mice. To achieve this, we combined the use of: (i) a hyperactive codon-optimized piggyBac transposase, (ii) a computationally enhanced liver-specific promoter, (iii) a hyperfunctional codon-optimized FIX transgene (FIX R338L Padua), and (iv) a modification of the transposon terminal repeats. This combination strategy resulted in a robust 400-fold improvement in vector performance in hepatocytes, yielding stable supraphysiologic human FIX activity (>1 year). Liver-specific expression resulted in the induction of FIX-specific immune tolerance. Remarkably, only very low transposon/transposase doses were required to cure the bleeding diathesis. Similarly, PB transposons could be used to express supraphysiologic factor VIII levels using low transposon/transposase doses. PB transposition did not induce tumors in a sensitive hepatocellular carcinoma-prone mouse model. These results underscore the potency and relative safety of the latest generation PB transposons, which constitutes a versatile platform for stable and robust secretion of therapeutic proteins. PMID:25034357

  4. Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC).

    PubMed

    Hubner, Nina C; Mann, Matthias

    2011-04-01

    Large-scale proteomic screens are increasingly employed for placing genes into specific pathways. Therefore generic methods providing a physiological context for protein-protein interaction studies are of great interest. In recent years many protein-protein interactions have been determined by affinity purification followed by mass spectrometry (AP-MS). Among many different AP-MS approaches, the recently developed Quantitative BAC InteraCtomics (QUBIC) approach is particularly attractive as it uses tagged, full-length baits that are expressed under endogenous control. For QUBIC large cell line collections expressing tagged proteins from BAC transgenes or gene trap loci have been developed and are freely available. Here we describe detailed workflows on how to obtain specific protein binding partners with high confidence under physiological conditions. The methods are based on fast, streamlined and generic purification procedures followed by single run liquid chromatography-mass spectrometric analysis. Quantification is achieved either by the stable isotope labeling of amino acids in cell culture (SILAC) method or by a 'label-free' procedure. In either case data analysis is performed by using the freely available MaxQuant environment. The QUBIC approach enables biologists with access to high resolution mass spectrometry to perform small and large-scale protein interactome mappings. PMID:21184827

  5. Precision genome editing in plants via gene targeting and piggyBac-mediated marker excision

    PubMed Central

    Nishizawa-Yokoi, Ayako; Endo, Masaki; Ohtsuki, Namie; Saika, Hiroaki; Toki, Seiichi

    2015-01-01

    Precise genome engineering via homologous recombination (HR)-mediated gene targeting (GT) has become an essential tool in molecular breeding as well as in basic plant science. As HR-mediated GT is an extremely rare event, positive–negative selection has been used extensively in flowering plants to isolate cells in which GT has occurred. In order to utilize GT as a methodology for precision mutagenesis, the positive selectable marker gene should be completely eliminated from the GT locus. Here, we introduce targeted point mutations conferring resistance to herbicide into the rice acetolactate synthase (ALS) gene via GT with subsequent marker excision by piggyBac transposition. Almost all regenerated plants expressing piggyBac transposase contained exclusively targeted point mutations without concomitant re-integration of the transposon, resulting in these progeny showing a herbicide bispyribac sodium (BS)-tolerant phenotype. This approach was also applied successfully to the editing of a microRNA targeting site in the rice cleistogamy 1 gene. Therefore, our approach provides a general strategy for the targeted modification of endogenous genes in plants. PMID:25284193

  6. BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins.

    PubMed

    Selvaraj, MuthuKrishnan; Puri, Munish; Dikshit, Kanak L; Lefevre, Christophe

    2016-01-01

    The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL) proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Support vector machine (SVM) models were developed for predicting HbL proteins based upon amino acid composition (AC), dipeptide composition (DC), hybrid method (AC + DC), and position specific scoring matrix (PSSM). In addition, we introduce for the first time a new prediction method based on max to min amino acid residue (MM) profiles. The average accuracy, standard deviation (SD), false positive rate (FPR), confusion matrix, and receiver operating characteristic (ROC) were analyzed. We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques. Prediction accuracy was further investigated through confusion matrix and ROC curve analysis. All experimental results indicate that the proposed BacHbpred can be a perspective predictor for determination of HbL related proteins. BacHbpred, a web tool, has been developed for HbL prediction. PMID:27034664

  7. Analysis of chromosome conservation in Lemur catta studied by chromosome paints and BAC/PAC probes.

    PubMed

    Cardone, Maria Francesca; Ventura, Mario; Tempesta, Sergio; Rocchi, Mariano; Archidiacono, Nicoletta

    2002-12-01

    A panel of human chromosome painting probes and bacterial and P1 artificial chromosome (BAC/PAC) clones were used in fluorescence in situ hybridization (FISH) experiments to investigate the chromosome conservation of the ring-tailed lemur (Lemur catta, LCA) with respect to human. Whole chromosome paints specific for human chromosomes 7, 9, 11, 13, 14, 17, 18, 20, 21, and X were found to identify a single chromosome or an uninterrupted chromosomal region in LCA. A large set of partial chromosome paints and BAC/PAC probes were then used to refine the characterization of the rearrangements differentiating the two karyotypes. The results were also used to reconstruct the ancestral Lemuridae karyotype. Lemur catta, indeed, can be used as an outgroup, allowing symplesiomorphic (ancestral) rearrangements to be distinguished from apomorphic (derived) rearrangements in lemurs. Some LCA chromosomes are difficult to distinguish morphologically. The 'anchorage' of most LCA chromosomes to specific probes will contribute to the standardization of the karyotype of this species. PMID:12474064

  8. Clinical comparison of the isolator and BacT/Alert aerobic blood culture systems.

    PubMed Central

    Hellinger, W C; Cawley, J J; Alvarez, S; Hogan, S F; Harmsen, W S; Ilstrup, D M; Cockerill, F R

    1995-01-01

    The performance characteristics of the Isolator (Wampole Laboratories, Cranbury, N.J.) and the BacT/Alert (Organon Teknika Corporation, Durham, N.C.) aerobic blood culture systems were compared for 6,009 blood culture sets obtained from patients with suspected bloodstream infections. The BacT/Alert aerobic bottle [BTA(O2)] was continuously agitated while it was incubated in 5% CO2 at 36 degrees C; culture plates prepared from the Isolator tube [I(O2)] were incubated in 5% CO2 at 37 degrees C. From 394 blood cultures, 416 clinically significant isolates of bacteria and yeasts were recovered. The overall yields for BTA(O2) and I(O2) were not significantly different (319 versus 336; P = 0.20). I(O2) recovered significantly more staphylococcus (P < 0.05) and yeast isolates (P < 0.01). BTA(O2) recovered significantly more aerobic and facultatively anaerobic gram-negative bacilli (P < 0.05). In blood culture sets which produced growth of the same organisms in both the BTA(O2) and I(O2) systems, the BTA(O2) system detected growth sooner, but more rapid identification was possible with the I(O2) system by virtue of earlier isolation of colonies on solid media. PMID:7665647

  9. Novel glycoside hydrolases identified by screening a Chinese Holstein dairy cow rumen-derived metagenome library.

    PubMed

    Zhao, Shengguo; Wang, Jiaqi; Bu, Dengpan; Liu, Kailang; Zhu, Yaxin; Dong, Zhiyang; Yu, Zhongtang

    2010-10-01

    One clone encoding glycoside hydrolases was identified through functional screening of a rumen bacterial artificial chromosome (BAC) library. Of the 68 open reading frames (ORFs) predicted, one ORF encodes a novel endo-β-1,4-xylanase with two catalytic domains of family GH43 and two cellulose-binding modules (CBMs) of family IV. Partial characterization showed that this endo-xylanase has a greater specific activity than a number of other xylanases over a wide temperature range at neutral pH and could be useful in some industrial applications. PMID:20709844

  10. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: BAC-based physical maps provide for sequencing across an entire genome or selected sub-genome regions of biological interest. Using the minimum tiling path as a guide, it is possible to select specific BAC clones from prioritized genome sections such as a genetically defined QTL interv...

  11. Efficacy of a BAC clone of a recombinant strain of Marek’s disease virus containing reticuloendotheliosis virus LTR following in ovo Vaccination at 18 days of embryonation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have previously reported on the pathogenicity of various passage levels of a bacterial artificial chromosome (BAC) clone of a recombinant Marek’s disease virus (MDV) strain rMd5 containing reticuloendotheliosis virus (REV) long terminal repeat (LTR) termed rMd5 REV LTR BAC. In this study, we eval...

  12. DNA sequences and composition from 12 BAC clones-derived MUSB SSR markers mapped to cotton (Gossypium Hirsutum L. x G. Barbadense L.)chromosomes 11 and 21

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To discover resistance (R) and/or pathogen-induced (PR) genes involved in disease response, 12 bacterial artificial chromosome (BAC) clones from cv. Acala Maxxa (G. hirsutum) were sequenced at the Clemson University, Genomics Institute, Clemson, SC. These BACs derived MUSB single sequence repeat (SS...

  13. Controlled comparison of the BacT/Alert and BACTEC 660/730 nonradiometric blood culture systems.

    PubMed Central

    Wilson, M L; Weinstein, M P; Reimer, L G; Mirrett, S; Reller, L B

    1992-01-01

    In a collaborative study at three university hospitals, the recovery of microorganisms and the speed of detection of microbial growth by the BacT/Alert (Organon Teknika Corporation, Durham, N.C.) and BACTEC 660/730 (Becton-Dickinson Diagnostic Instrument Systems, Sparks, Md.) nonradiometric blood culture systems were compared. A total of 5,918 comparisons were made between BacT/Alert aerobic and BACTEC NR 6A bottles and 5,992 comparisons were made between BacT/Alert anaerobic and BACTEC NR 7A bottles. Each bottle was inoculated with 5 ml of blood. The overall recoveries of microorganisms from the two aerobic bottles were comparable; members of the family Enterobacteriaceae were recovered more often from BacT/Alert aerobic bottles alone (P less than 0.001). The overall recoveries of microorganisms from the anaerobic bottles were not significantly different. Growth of Staphylococcus aureus (P less than 0.001), coagulase-negative staphylococci (P less than 0.01), streptococci (P less than 0.001), Escherichia coli (P less than 0.01), other members of the family Enterobacteriaceae (P less than 0.02), and Pseudomonas aeruginosa (P less than 0.05) was detected earlier in BacT/Alert aerobic bottles. Growth of S. aureus (P less than 0.001), coagulase-negative staphylococci (P less than 0.05), enterococci (P less than 0.01), Streptococcus pneumoniae (P less than 0.02), viridans group streptococci (P less than 0.05), E. coli (P less than 0.001), Klebsiella pneumoniae (P less than 0.01), and other members of the family Enterobacteriaceae (P less than 0.001) was detected earlier in BacT/Alert anaerobic bottles. In a system-versus-system comparison, more gram-positive cocci were recovered from the BACTEC system alone (P < 0.05), and more members or the family Enterobacteriaceae were recovered from the BacT/Alert system alone (P < 0.001). As a system, the BacT/Alert system detected growth of S. aureus (P < 0.001), coagulase-negative staphylococci (P < 0.01), streptococci (P < 0

  14. Rhode Island Library Trustees Manual.

    ERIC Educational Resources Information Center

    Iacono, Frank P., Ed.

    This handbook for library trustees identifies the duties and responsibilities of library boards and librarians, the qualifications of an effective library and of a library board, and library policy requirements. The concept of intellectual freedom, the Library Bill of Rights, and the Freedom to Read Statement are discussed, and the role of the…

  15. Planning & Urban Affairs Library Manual.

    ERIC Educational Resources Information Center

    Knobbe, Mary L., Ed.; Lessel, Janice W., Ed.

    Written especially for persons without a library degree who are operating a small urban study or planning agency library on a part-time basis. Subjects covered are: (1) library function and staff function, duties and training; (2) physical layout and equipment of library; (3) establishing and maintaining the library; (4) library administration;…

  16. Flight Software Math Library

    NASA Technical Reports Server (NTRS)

    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.

  17. Assessing Library Automation and Virtual Library Development in Four Academic Libraries in Oyo, Oyo State, Nigeria

    ERIC Educational Resources Information Center

    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…

  18. IAC Library: Some Challenges

    NASA Astrophysics Data System (ADS)

    Gomez, M.

    2010-10-01

    Since its beginnings in 1985, the IAC Library has evolved from a traditional library where the physical place and collections were essential, to a hybrid library where users can often get what they need without going to the library. In this paper, we present how the various changes due to information technology advances that occurred in the 1990s, followed by a series of works carried out from 2004 to 2008 at IAC, as well as several internal and external events or decisions, have led the IAC Library to face three new challenges. First, as the library building has been enlarged and new spaces are now available for users and for shelving, we have to decide what we should we do with the new spaces. How we can make them attractive for users at a time when users often don't need to visit the library to access the information they need? Second, as IAC will implement a new integrated information system, we have an opportunity to define how the library system will participate within the IAC global information system, bringing to this great project our knowledge of information management, essential to improve the actual processes. Third, as the Ministry has created a working group on access to electronic resources, with participation by seven affiliated research institutions, we have, as a member of this group, to define how to deal with the Ministry and the other centres to set a library policy that will benefit the IAC Library.

  19. Germline transformation of the olive fruit fly, Bactrocera oleae (Rossi)(Diptera:Tephritidae) with a piggyBac transposon vector

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The olive fruit fly, Bactrocera oleae, is a highly significant pest in olive growing countries whose control may be enhanced by the use of genetically-modified strains, especially for sterile insect technique programs. To improve and expand this technology, piggyBac-mediated germline transformation ...

  20. Highly similar piggyBac elements in Bactrocera that share a common lineage with elements in noctuid moths

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The piggyBac IFP2 transposable element, originally discovered in a Trichoplusia ni cell line, also exists as nearly identical elements in other noctuid lepidopteran species and in mutant and wild type strains of the oriental fruit fly, Bactrocera dorsalis. To further define the distribution of pigg...

  1. Development of a Set of Chromosome-Specific Cytogenetic DNA Markers in Sunflower Using BAC-FISH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In diploid sunflower (2n=34), conventional karyotypes and various genetic linkage maps have been established. However, the relationship between genetic linkage groups and individual chromosomes of sunflower remains unknown. Recently, a set of linkage group-specific BAC and BIBAC clones were identifi...

  2. THE WHEAT D-GENOME HMW-GLUTENIN LOCUS:BAC SEQUENCING, GENE DISTRIBUTION, AND RETROTRANSPOSON CLUSTERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A bacterial-artificial-chromosome (BAC) clone from the genome of Triticum tauschii, the D-genome ancestor of hexaploid bread wheat, was sequenced and the presence of the two paralogous x- and y- type high-molecular-weight (HMW) glutenin genes of the Glu-D1 locus was confirmed. These two genes occur...

  3. Development of Health Education Learning Module in Bac.TSE-LDPE Programme in TTI: Needs Analysis Study

    ERIC Educational Resources Information Center

    Ujang, Alijah; Alias, Norlidah; Siraj, Saedah

    2015-01-01

    This study is to explore the need to develop learning modules of health education for trainee teachers in the Bachelor Of Teaching (Hons)(Special Education-Learning Disabilities For Primary Education) Programme (Bac.TSE-LDPE) in the Teacher Training Institute (TTI). The questionnaire uses the Likert scale with the close ended questions analysed by…

  4. Application of the BAC-MP4 method and its variations in determining thermochemical properties of molecules

    SciTech Connect

    Melius, C.F.

    1996-12-31

    The Bond-Additivity-Corrected Moller-Plesset 4th order perturbation theory method (BAC-NW4) has demonstrated its ability to provide accurate thermochemical properties of small gas-phase molecules (up to eight heavy atoms plus hydrogens). Such properties include the enthalpies, entropies, free energies, etc. for both radicals and closed-shell stable species as well as for transition-state structures. This has enabled one to calculate useful reaction rates for gas-phase molecules. To improve the accuracy of the BAC method, variations have been developed, such as using the MP2 method for geometry optimizations rather than the Hartree-Fock method, and using larger basis sets for the MP4 step. In order to treat larger molecules, the NW2 method has been used for the single-point energy step (i.e., BAC-MP2). In this paper, we discuss the objectives and limitations of the BAC paradigm and its future development directions. In particular, we present means to treat larger molecules, disparate oxidation states, and heavier-Z elements.

  5. Monochloramine disinfection kinetics of Nitrosomonas europaea by propidium monoazide quantitative PCR and Live/Dead BacLight Methods

    EPA Science Inventory

    Monochloramine disinfection kinetics were determined for the pure culture ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) by two culture independent methods: (1) LIVE/DEAD® BacLight™ (LD) and (2) propidium monoazide quantitative PCR (PMA-qPCR). Both methods were f...

  6. In vitro characterization of felid herpesvirus 1 (FHV-1) mutants generated by recombineering in a recombinant BAC vector

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Felid herpesvirus 1 (FHV-1) mutants were constructed using two-step Red-mediated recombination techniques based on a virulent full-length FHV-1 BAC clone. The individual mutant viruses generated were deficient in glycoprotein C (gC), glycoprotein E (gE),US3 serine/threonine protein kinase (PK), or b...

  7. Vast potential for using the piggyBac transposon to engineer transgenic plants at specific genomic locations.

    PubMed

    Johnson, Eric T; Owens, Jesse B; Moisyadi, Stefan

    2016-01-01

    The acceptance of bioengineered plants by some nations is hampered by a number of factors, including the random insertion of a transgene into the host genome. Emerging technologies, such as site-specific nucleases, are enabling plant scientists to promote recombination or mutations at specific plant loci. Off target activity of these nucleases may limit widespread use. Insertion of transgenes by transposases engineered with a specific DNA binding domain has been accomplished in a number of organisms, but not in plants. The piggyBac transposon system, originally isolated from an insect, has been utilized to transform a variety of organisms. The piggyBac transposase is amendable to structural modifications, and was able to insert a transgene at a specific human locus through fusion of a DNA binding domain to its N-terminus. Recent developments demonstrating the activity of piggyBac transposase in plants is an important first step toward the potential use of engineered versions of piggyBac transposase for site-specific transgene insertion in plants. PMID:26930269

  8. Data quality management system (DQMS) for BAC detector in the ZEUS experiment at the HERA accelerator

    NASA Astrophysics Data System (ADS)

    Luszczak, Zbigniew; Jezynski, Tomasz; Romaniuk, Ryszard S.; Pozniak, Krzysztof T.; Kuthan, Marcin; Bigos, Grzegorz; Gierej, Artur

    2003-10-01

    The paper presents functional structure of database system of data measurement quality for BAC detector in ZEUS experiment. The system collects diagnostic and experimental data. Diagnostic data are: work parameters of the detector and electronics/photonics, tests of electronic/photonic blocks. These data are archived for certain period of time. The quality of current data collection process is estimated using these archived data. The result of such estimation is generated in a form of status map of the detector. Such maps, describing status of the hardware, are fundamental for elementary particle analysis by the calorimeter. The DAQ system, collecting data to the database, estimates data quality on-line during transmission and writing. This mechanism of fast on-line data quality management leads to early discoveries of detector work irregularities and faults.

  9. PiggyBac transposon vectors: the tools of the human gene encoding

    PubMed Central

    Zhao, Shuang; Jiang, Enze; Chen, Shuangshuang; Gu, Yuan; Shangguan, Anna Junjie; Lv, Tangfeng

    2016-01-01

    A transposon is a DNA segment, which is able to change its relative position within the entire genome of a cell. The piggyBac (PB) transposon is a movable genetic element that efficiently transposes between vectors and chromosomes through a “cut-and-paste” mechanism. During transposition, the PB transposase recognizes transposon-specific inverted terminal repeats (ITRs) sequences located on both ends of the transposon vector and eight efficiently moves the contents from its original positions and efficiently integrates them into TTAA chromosomal sites. PB has drawn much attention because of its transposition efficiency, safety and stability. Due to its priorities, PB can be used as a new genetic vehicle, a new tool for oncogene screening and a new method for gene therapy. PB has created a new outlook for human gene encoding. PMID:26958506

  10. Microbial Community Structures and Dynamics in the O3/BAC Drinking Water Treatment Process

    PubMed Central

    Tian, Jian; Lu, Jun; Zhang, Yu; Li, Jian-Cheng; Sun, Li-Chen; Hu, Zhang-Li

    2014-01-01

    Effectiveness of drinking water treatment, in particular pathogen control during the water treatment process, is always a major public health concern. In this investigation, the application of PCR-DGGE technology to the analysis of microbial community structures and dynamics in the drinking water treatment process revealed several dominant microbial populations including: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Actinobacteria Firmicutes and Cyanobacteria. α-Proteobacteria and β-Proteobacteria were the dominant bacteria during the whole process. Bacteroidetes and Firmicutes were the dominant bacteria before and after treatment, respectively. Firmicutes showed season-dependent changes in population dynamics. Importantly, γ-Proteobacteria, which is a class of medically important bacteria, was well controlled by the O3/biological activated carbon (BAC) treatment, resulting in improved effluent water bio-safety. PMID:24937529

  11. libdrdc: software standards library

    NASA Astrophysics Data System (ADS)

    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.

  12. Integrated circuit cell library

    NASA Technical Reports Server (NTRS)

    Whitaker, Sterling R. (Inventor); Miles, Lowell H. (Inventor)

    2005-01-01

    According to the invention, an ASIC cell library for use in creation of custom integrated circuits is disclosed. The ASIC cell library includes some first cells and some second cells. Each of the second cells includes two or more kernel cells. The ASIC cell library is at least 5% comprised of second cells. In various embodiments, the ASIC cell library could be 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, 60% or more, 70% or more, 80% or more, 90% or more, or 95% or more comprised of second cells.

  13. Malta: The Library Scene and its Setting

    ERIC Educational Resources Information Center

    Biggs, P. T.

    1973-01-01

    The cultural background of Malta is briefly analyzed as it relates to library service on the island. The library system includes public libraries, university libraries, religious libraries and special libraries. (39 references) (DH)

  14. Public Relations in Special Libraries.

    ERIC Educational Resources Information Center

    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…

  15. FCLib: The Feature Characterization Library.

    SciTech Connect

    Gentile, Ann C.; Doyle, Wendy S. K.; Kegelmeyer, W. Philip; Ulmer, Craig D.

    2008-11-01

    The Feature Characterization Library (FCLib) is a software library that simplifies the process of interrogating, analyzing, and understanding complex data sets generated by finite element applications. This document provides an overview of the library, a description of both the design philosophy and implementation of the library, and examples of how the library can be utilized to extract understanding from raw datasets.

  16. Library Latchkey Children. ERIC Digest.

    ERIC Educational Resources Information Center

    Dowd, Frances Smardo

    This digest discusses ways in which public libraries deal with latchkey children who spend their after-school hours at public libraries while their parents are at work. Research conducted in 1990 of 110 public libraries revealed that almost all libraries encountered unattended children after school hours, and that most libraries surveyed were not…

  17. Resources of North Carolina Libraries.

    ERIC Educational Resources Information Center

    Downs, Robert B., Ed.

    The conclusion of the survey is that North Carolina libraries do not have sufficient resources, physical facilities or staff to provide adequate library service for the state. The survey covers the present and potential roles of the State Library, the State Department of Archives and History, public libraries, university libraries, senior and…

  18. Optical Disc Applications in Libraries.

    ERIC Educational Resources Information Center

    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…

  19. Idaho's Library Future.

    ERIC Educational Resources Information Center

    Idaho State Library, Boise.

    In l998, Idahoans gathered in a series of six Regional Futures Conferences to identify what they thought was probable during the next ten years, what was possible for libraries to do and be, and what a preferred future of Idaho libraries might be. Participants from the regional conferences then convened to refine and focus descriptions of the…

  20. Library Consortia in Hungary

    ERIC Educational Resources Information Center

    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…

  1. Using Your Library Effectively.

    ERIC Educational Resources Information Center

    Hennepin County Library, Minnetonka, MN.

    This collection of materials for a three-hour instructional program for young people and adults in the effective use of the public library includes an introduction to the program, a teaching guide for the librarian, a packet of materials for students, and a summary of 90 evaluations of the program as it was presented at two area libraries and…

  2. Small Public Library Management

    ERIC Educational Resources Information Center

    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…

  3. Disaster Planning in Libraries

    ERIC Educational Resources Information Center

    Wong, Yi Ling; Green, Ravonne

    2006-01-01

    Disaster preparedness is an important issue in library management today. This article presents a general overview of the theoretical aspects of disaster planning in libraries. The stages of disaster planning are a circular process of planning, prevention, response, recovery, preparedness, and training.

  4. Image-analysis library

    NASA Technical Reports Server (NTRS)

    1980-01-01

    MATHPAC image-analysis library is collection of general-purpose mathematical and statistical routines and special-purpose data-analysis and pattern-recognition routines for image analysis. MATHPAC library consists of Linear Algebra, Optimization, Statistical-Summary, Densities and Distribution, Regression, and Statistical-Test packages.

  5. The Library as Ecosystem

    ERIC Educational Resources Information Center

    Walter, Scott

    2008-01-01

    Ecology is the study of interactions between organisms and their environment, and the academic library could be considered to be an ecosystem, i.e., a "biological organization" in which multiple species must interact, both with one another and with their environment. The metaphor of the library as ecosystem is flexible enough to be applied not…

  6. Libraries at the Ready

    ERIC Educational Resources Information Center

    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…

  7. LSCA Builds Michigan Libraries.

    ERIC Educational Resources Information Center

    Michigan Library, Lansing.

    This report highlights 19 of the 48 recently completed public library construction projects in Michigan which received partial funding from the 1983 Emergency Jobs Act. The grants were administered under Title II of the Library Services and Construction Act (LSCA). Introductory material includes listings of the State of Michigan Legislative…

  8. The Undergraduate Library Collection.

    ERIC Educational Resources Information Center

    Stewart, Rolland C.

    The development of undergraduate library collections is shown under two aspects: (1) the formation of the basic collection of the Undergraduate Library of the University of Michigan, and (2) the problems, practical and theoretial, encountered in the day-to-day effort to maintain the collection. The budget is the sire of all selection criteria.…

  9. "Greening" up the Library

    ERIC Educational Resources Information Center

    Woodland, Jean

    2010-01-01

    This paper looks at the library's ability to spread environmental conservation efforts throughout the community. The paper suggests various ways library staff can explore environmentally friendly procedures within the context of the media center as well as ways to promote community interest and support. It identifies areas for improvement, ideas…

  10. Academic Libraries in Japan

    ERIC Educational Resources Information Center

    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. Library Automation Style Guide.

    ERIC Educational Resources Information Center

    Gaylord Bros., Liverpool, NY.

    This library automation style guide lists specific terms and names often used in the library automation industry. The terms and/or acronyms are listed alphabetically and each is followed by a brief definition. The guide refers to the "Chicago Manual of Style" for general rules, and a notes section is included for the convenience of individual…

  12. Hospital Library Administration.

    ERIC Educational Resources Information Center

    Cramer, Anne

    The objectives of a hospital are to improve patient care, while the objectives of a hospital library are to improve services to the staff which will support their efforts. This handbook dealing with hospital administration is designed to aid the librarian in either implementing a hospital library, or improving services in an existing medical…

  13. Ubibliotheca The Spiral Library.

    ERIC Educational Resources Information Center

    Ottewell, Guy

    A plan for a library with a storage level in the shape of a flat spiral is presented. The advantages of such a plan include: space saving, easy expansion of the building, an unbroken sequence of shelving, quick access to all books and freedom in the design of the library's other sectors. This plan is especially suited for the research library…

  14. University Libraries in Transition.

    ERIC Educational Resources Information Center

    Hyatt, James A.

    1986-01-01

    College and university libraries are experiencing change in the ways they provide services and in their responses to rising costs and reduced financial support. These conditions result from three major phenomena: the information explosion, the technology revolution, and escalating library costs. (MLW)

  15. Facility Focus: Libraries.

    ERIC Educational Resources Information Center

    College Planning & Management, 1997

    1997-01-01

    Describes four operating libraries located at Union Theological Seminary in Virginia, Emory University in Georgia, Kean College in New Jersey, and Community College of Philadelphia. Their size, cost, date completed, architect, and various features are provided. Despite technological advances, the college library is a feasible part of higher…

  16. Attribution of Library Costs

    ERIC Educational Resources Information Center

    Drake, Miriam A.

    1977-01-01

    Universities conduct a variety of cost-allocation studies that require the collection and analysis of the library cost-data. Cost accounting methods are used in most studies; however, costs are attributed to library user groups in a variety of ways. Cost accounting studies are reviewed and allocation methods are discussed. (Author)

  17. Maintaining Precious Library Resources.

    ERIC Educational Resources Information Center

    Wiens, Janet

    2002-01-01

    Using the examples of libraries at Southeast Missouri State University and the University of North Texas, discusses the big-picture approach and extensive communication among all users necessary for library maintenance efforts. Addresses establishing a master plan, prioritizing projects, having the right staff, and communicating. (EV)

  18. FRBR and School Libraries

    ERIC Educational Resources Information Center

    Hart, Amy

    2006-01-01

    This article discusses the Functional Requirements for Bibliographic Records (FRBR), a plan that is quickly gaining the support of library organizations around the globe. The FRBR Study Group was appointed by International Federation of Library Associations (IFLA) and issued its final report in 1998. The report redefines the basic unit of…

  19. Online Library Videos

    ERIC Educational Resources Information Center

    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…

  20. An Online Library Catalogue.

    ERIC Educational Resources Information Center

    Alloro, Giovanna; Ugolini, Donatella

    1992-01-01

    Describes the implementation of an online catalog in the library of the National Institute for Cancer Research and the Clinical and Experimental Oncology Institute of the University of Genoa. Topics addressed include automation of various library functions, software features, database management, training, and user response. (10 references) (MES)

  1. Library Resources Workbook, Revised.

    ERIC Educational Resources Information Center

    Phillips, Dennis

    Intended to provide a basic overview of the facilities and resources of the library on the Allentown Campus of Pennsylvania State University, this student workbook is designed to familiarize students with what is available to them in the library; to introduce them to skills likely to be used in varying degrees throughout life, regardless of what…

  2. Homelessness in Public Libraries

    ERIC Educational Resources Information Center

    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…

  3. Library Technician Skill Standards.

    ERIC Educational Resources Information Center

    Highline Community Coll., Des Moines, WA.

    This document presents skill standards for library technicians. Introductory sections describe the industry and the job, what skill standards are, how the library technician skill standards were developed, employability skills and critical competencies, and the SCANS (Secretary's Commission on Achieving Necessary Skills) foundation skills profile.…

  4. Privacy and Library Records

    ERIC Educational Resources Information Center

    Bowers, Stacey L.

    2006-01-01

    This paper summarizes the history of privacy as it relates to library records. It commences with a discussion of how the concept of privacy first originated through case law and follows the concept of privacy as it has affected library records through current day and the "USA PATRIOT Act."

  5. Academic Libraries in Iran

    ERIC Educational Resources Information Center

    Deale, H. Vail

    1973-01-01

    Iranian librarianship is in the embryonic stages of development, especially with respect to modern and functional academic libraries. In three major areas--personnel, resources, and physical facilities--the academic libraries are deficient compared with Western standards. (16 references) (Author)

  6. Centennial State Libraries, 1998.

    ERIC Educational Resources Information Center

    Parent, Kathleen D., Ed.

    1998-01-01

    This document consists of 12 consecutive issues of the monthly "Centennial State Libraries" newsletter, of the Colorado Department of Education, State Library and Adult Education Office. The issues cover the year 1998. Each issue of the newsletter--except the August issue which is an Annual Report--includes some or all of the following sections:…

  7. Dumping the "Library."

    ERIC Educational Resources Information Center

    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…

  8. Library Reference Services.

    ERIC Educational Resources Information Center

    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…

  9. Merchandising Techniques and Libraries.

    ERIC Educational Resources Information Center

    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)

  10. Library Classification 2020

    ERIC Educational Resources Information Center

    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…

  11. Libraries and Adult Learners.

    ERIC Educational Resources Information Center

    Josey, E. J., Ed.

    1982-01-01

    Of the 13 essays presented in this special issue on libraries and adult education, 8 focus on programs and services from the public library for adult learners. These essays provide information on: (1) an Education Information Centers Program (EIC) designed to complement employment skills training provided under the Comprehensive Employment and…

  12. XML in Libraries.

    ERIC Educational Resources Information Center

    Tennant, Roy, Ed.

    This book presents examples of how libraries are using XML (eXtensible Markup Language) to solve problems, expand services, and improve systems. Part I contains papers on using XML in library catalog records: "Updating MARC Records with XMLMARC" (Kevin S. Clarke, Stanford University) and "Searching and Retrieving XML Records via the Web" (Theo van…

  13. Libraries, Listservs, and LITA.

    ERIC Educational Resources Information Center

    Williams, Brian

    1992-01-01

    Explains a series of 39 slides used in a presentation covering guides to libraries on the Internet computer network; other INTERNET resources, including bibliographic databases, catalogs, and online services; BITNET servers and LISTSERVS, and the MicroUser's computer conference sponsored by the Library and Information Technology Association…

  14. Library Web Site Innovations.

    ERIC Educational Resources Information Center

    Falk, Howard

    1999-01-01

    Reports on some of the new ways public library sites are presenting themselves to their patrons and to the broader World Wide Web audience. Discusses library virtual tours; calendar display; audio-visual materials; resource listings; book clubs; money-raising activities; fugitive fact files; hot item advisors; periodicals; FAQs (frequently asked…

  15. Guidelines on Library Twinning.

    ERIC Educational Resources Information Center

    Doyle, Robert P., Comp.; Scarry, Patricia, Comp.

    This document serves as an overview of the many forms of library twinning, or formal exchanges of materials and/or staff between two institutions. Twinning can be reciprocal, but often involves a one-way arrangement whereby a library in a developing country receives a visit from a librarian of a developed country. Either way, both institutions can…

  16. Improving Library Research Skills.

    ERIC Educational Resources Information Center

    Holley, Catherine W.

    This report describes a program to advance library research skills in two sixth grade science classes. The problem was assessed through a survey, questionnaire, and worksheet, and by direct observation. Analysis of probable cause data revealed that students displayed a lack of research skills related to library research. Some of the causes were…

  17. Library Connection Development.

    ERIC Educational Resources Information Center

    Berry, John N., III

    1990-01-01

    The John Wiley and Sons publishing company has made a commitment to publishing more tradebooks for the retail and library marketplace. As part of this expansion, Wiley has strengthened its library sales and promotion efforts and launched new publications and promotions to reach librarians. (MES)

  18. Guidelines for National Libraries.

    ERIC Educational Resources Information Center

    Sylvestre, Guy

    This report is designed to provide practical assistance to government officials and librarians responsible for the planning, creation, and development of national library services. Based on a number of authoritative studies and a broad consensus among experts, including directors of national libraries, these guidelines give special attention to…

  19. Libraries for Small Museums.

    ERIC Educational Resources Information Center

    Anderson, Linda M.

    Presented are the very basic requirements for establishing a small special library operating under a limited budget. Physical plant organization, cataloging, book processing, circulation procedures, book selection and ordering and instructions for typists are covered. Although the practices discussed were established for a museum library, what is…

  20. The Amazing Library Computer.

    ERIC Educational Resources Information Center

    Anderson, Eric S.

    1983-01-01

    Identifies computer software designed specifically for library management tasks in three distinct categories: library utility programs, and circulation and catalog programs for floppy disk and for hard disk. Company name and address, program, application, hardware, cost, and comments are provided in each category. (EJS)

  1. Networking among Chevron Libraries.

    ERIC Educational Resources Information Center

    Linden, Margaret J.

    1989-01-01

    Describes the process by which librarians at the Chevron and Gulf Oil Corporations managed the merger of corporation libraries and developed a framework for a company-wide library network. The discussion covers corporate policies for information exchange, shared resources, and cost control, and examines factors that led to the success of the…

  2. Global Warming's Library Challenge

    ERIC Educational Resources Information Center

    Meyer, Jennifer

    2008-01-01

    Like every institution that uses energy, consumes resources, and engages in construction or renovation, libraries have an impact on the environment and on the critical problem of climate change. Taking action to protect library collections is not only an idealistic professional goal but also a very practical one. Disaster preparation measures and…

  3. Libraries: Drawn to Knowledge.

    ERIC Educational Resources Information Center

    Havens, Kevin

    2003-01-01

    Discusses how to make a college library the center of campus activity, explaining how to find the proper balance of technology and tradition (e.g., harnessing new media to teach critical thinking skills, having library staff assume primary responsibility for providing information literacy training, training students to use print as well as…

  4. The Animated Library

    ERIC Educational Resources Information Center

    Brewer, Jim; Dyal, Donald H.; Sweet, Robert

    2009-01-01

    Libraries have always been poised at the crossroads of access tools and content. Librarians, their personnel, and supporters have worked for generations to create tools to store and utilize content for the benefit of patrons. Libraries house materials and the tools to unlock them; their staffers teach patrons to use the materials and associated…

  5. Library Technology International

    ERIC Educational Resources Information Center

    Breeding, Marshall

    2008-01-01

    The author has been extremely fortunate over the last few years to have had the opportunity to travel to many different parts of the world and speak and work with librarians in many countries and to have the chance to see first-hand some incredible libraries that demonstrate creative approaches to library services, innovative uses of technology,…

  6. Technion Libraries Systems Study.

    ERIC Educational Resources Information Center

    Thomas, Pauline

    This study is aimed at clarifying the objectives of the Technion Libraries' Systems, both within the Technion and as a national information resource, by defining the structure, organization, and methods to achieve these objectives. It considers Technion's future plans and current library practices as based on reports on the system, Technion…

  7. The Underground Library.

    ERIC Educational Resources Information Center

    American School and University, 1983

    1983-01-01

    Recessed 25 feet below grade, the library at the Lawrence Institute of Technology has a garden area below the light well. A large atrium with four skylights above the library serves as a buffer zone and an informal gathering place. (Author/MLF)

  8. When a Library Closes.

    ERIC Educational Resources Information Center

    Griffin, Mary Ann

    1984-01-01

    This review of case studies of five academic libraries in institutions that have ceased operation notes background, time factors, disposition of library collections, and nature of bankruptcy. Guidelines for closing (stabilizing and documenting collection, estimating worth of collection, obligations to government) are presented. Eight sources are…

  9. Computer Based Library Orientation.

    ERIC Educational Resources Information Center

    Machalow, Robert

    This document presents computer-based lessons used to teach basic library skills to college students at York College of the City University of New York. The information for library orientation has been entered on a disk which must be used in conjunction with a word processing program, the Applewriter IIe, and an Apple IIe microcomputer. The…

  10. Outreach Library Services.

    ERIC Educational Resources Information Center

    The Bookmark, 1985

    1985-01-01

    Focusing on the theme, Outreach Library Services, the articles in this publication provide a panoramic view of outreach services in eight of the public library systems in New York State. The compilation also contains four papers on special topics. Articles included are: (1) "Not So Trivial: In Pursuit of Outreach Services" (Joan F. Cooke, Finger…

  11. Budgeting for Libraries.

    ERIC Educational Resources Information Center

    Randall, G. E.

    Empirically and rationally derived bases for determining the costs for industrial libraries are suggested. Taken into consideration is the fact that recent accounting procedures and the advent of new technologies have introduced costs into the library budget so that literature and personnel costs may now account for only 75-80 percent of the…

  12. Technology for Libraries.

    ERIC Educational Resources Information Center

    Phenix, Katharine; And Others

    1990-01-01

    Five articles discuss information technology in libraries: (1) "Software for Libraries" (Katharine Phenix); (2) "Online Update: European Online Services" (Martin Kesselman); (3) "Connect Time: Online Pricing Breakthroughs" (Barbara Quint); (4) "Microcomputing: Micro Biology Computer Viruses" (James LaRue); and (5) "Using Technology: Spreadsheet…

  13. Financing Public Library Construction.

    ERIC Educational Resources Information Center

    Rohlf, Robert H.; Stoffel, Lester L.

    1987-01-01

    Reviews financing options available to Illinois public libraries for construction or expansion, including general obligation bonds, mortgage funds, building reserve funds, building fund levies, lease back arrangements, sale of air or ground development rights, interest on special funds, gift funds and grants, Library Service and Construction Act…

  14. Fermilab Library projects

    SciTech Connect

    Garrett, P.; Ritchie, D.

    1990-05-03

    Preprint database management as done at various centers -- the subject of this workshop -- is hard to separate from the overall activities of the particular center. We therefore present the wider context at the Fermilab Library into which preprint database management fits. The day-to-day activities of the Library aside, the dominant activity at present is that of the ongoing Fermilab Library Automation. A less dominant but relatively time-consuming activity is that of doing more online searches in commercial databases on behalf of laboratory staff and visitors. A related activity is that of exploring the benefits of end-user searching of similar sources as opposed to library staff searching of the same. The Library Automation Project, which began about two years ago, is about to go fully online.'' The rationale behind this project is described in the documents developed during the December 1988--February 1989 planning phase.

  15. Administrative Libraries Section. Special Libraries Division. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    In "Contemporary Needs and Possibilities to Improve the Exchange of Bibliographical Information/Data Between Administrative Libraries (with Special Reference to Modern Technologies)," a discussion of the exchange of machine-readable bibliographic records, Walter Niedermeyr (Federal Republic of Germany) advocates the development of German…

  16. Fundamentals of Library Science. Library Science 424.

    ERIC Educational Resources Information Center

    Foster, Donald L.

    An introductory letter, a list of general instructions on how to proceed with a correspondence course, a syllabus, and an examination request form are presented for a correspondence course in the fundamentals of library science offered by the University of New Mexico's Division of Continuing Education and Community Services. The course is a survey…

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

    SciTech Connect

    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.

  18. Generation of a complete single-gene knockout bacterial artificial chromosome library of cowpox virus and identification of its essential genes.

    PubMed

    Xu, Zhiyong; Zikos, Dimitrios; Osterrieder, Nikolaus; Tischer, B Karsten

    2014-01-01

    Cowpox virus (CPXV) belongs to the genus Orthopoxvirus in the Poxviridae family. It infects a broad range of vertebrates and can cause zoonotic infections. CPXV has the largest genome among the orthopoxviruses and is therefore considered to have the most complete set of genes of all members of the genus. Since CPXV has also become a model for studying poxvirus genetics and pathogenesis, we created and characterized a complete set of single gene knockout bacterial artificial chromosome (BAC) clones of the CPXV strain Brighton Red. These mutants allow a systematic assessment of the contribution of single CPXV genes to the outcome of virus infection and replication, as well as to the virus host range. A full-length BAC clone of CPXV strain Brighton Red (pBRF) harboring the gene expressing the enhanced green fluorescent protein under the control of a viral late promoter was modified by introducing the mrfp1 gene encoding the monomeric red fluorescent protein driven by a synthetic early vaccinia virus promoter. Based on the modified BAC (pBRFseR), a library of targeted knockout mutants for each single viral open reading frame (ORF) was generated. Reconstitution of infectious virus was successful for 109 of the 183 mutant BAC clones, indicating that the deleted genes are not essential for virus replication. In contrast, 74 ORFs were identified as essential because no virus progeny was obtained upon transfection of the mutant BAC clones and in the presence of a helper virus. More than 70% of all late CPXV genes belonged to this latter group of essential genes. PMID:24155400

  19. Evaluation of a Plastic Nonvented Aerobic Blood Culture Bottle for Use with the BacT/ALERT Microbial Detection System

    PubMed Central

    Snyder, J. W.; Munier, G. K.; Bostic, G. D.; Bozigar, P. S.; Hanna, R.

    2002-01-01

    The current BacT/ALERT SA (BTA SA) aerobic blood culture bottle is made from glass, does not require venting, and contains a liquid emulsion sensor (LES). Its performance has been shown to be equivalent to that of the vented standard aerobic culture bottle. A further-improved version of the BTA SA bottle, designated the BacT/ALERT plastic SA (BTA PSA) culture bottle, is made from clear plastic to prevent breakage, does not require venting, and contains a modified LES (LES 2) to reduce the possibility of false positives. The BTA PSA provides a practical alternative to the current glass version of this bottle. The plastic bottle is also comparable to the current glass bottle in transparency and growth performance and additionally minimizes the exposure to infectious agents due to glass bottle breakage. PMID:12454188

  20. Novel Glycoside Hydrolases Identified by Screening a Chinese Holstein Dairy Cow Rumen-Derived Metagenome Library ▿ †

    PubMed Central

    Zhao, Shengguo; Wang, Jiaqi; Bu, Dengpan; Liu, Kailang; Zhu, Yaxin; Dong, Zhiyang; Yu, Zhongtang

    2010-01-01

    One clone encoding glycoside hydrolases was identified through functional screening of a rumen bacterial artificial chromosome (BAC) library. Of the 68 open reading frames (ORFs) predicted, one ORF encodes a novel endo-β-1,4-xylanase with two catalytic domains of family GH43 and two cellulose-binding modules (CBMs) of family IV. Partial characterization showed that this endo-xylanase has a greater specific activity than a number of other xylanases over a wide temperature range at neutral pH and could be useful in some industrial applications. PMID:20709844

  1. Marketing the hospital library.

    PubMed

    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. PMID:15982957

  2. The piggyBac Transposon-Mediated Expression of SV40 T Antigen Efficiently Immortalizes Mouse Embryonic Fibroblasts (MEFs)

    PubMed Central

    Cui, Jing; Zhang, Hongmei; Chen, Xiang; Li, Ruidong; Wu, Ningning; Chen, Xian; Wen, Sheng; Zhang, Junhui; Yin, Liangjun; Deng, Fang; Liao, Zhan; Zhang, Zhonglin; Zhang, Qian; Yan, Zhengjian; Liu, Wei; Ye, Jixing; Deng, Youlin; Wang, Zhongliang; Qiao, Min; Luu, Hue H.; Haydon, Rex C.; Shi, Lewis L.; Liang, Houjie; He, Tong-Chuan

    2014-01-01

    Mouse embryonic fibroblasts (MEFs) are mesenchymal stem cell (MSC)-like multipotent progenitor cells and can undergo self-renewal and differentiate into to multiple lineages, including bone, cartilage and adipose. Primary MEFs have limited life span in culture, which thus hampers MEFs’ basic research and translational applications. To overcome this challenge, we investigate if piggyBac transposon-mediated expression of SV40 T antigen can effectively immortalize mouse MEFs and that the immortalized MEFs can maintain long-term cell proliferation without compromising their multipotency. Using the piggyBac vector MPH86 which expresses SV40 T antigen flanked with flippase (FLP) recognition target (FRT) sites, we demonstrate that mouse embryonic fibroblasts (MEFs) can be efficiently immortalized. The immortalized MEFs (piMEFs) exhibit an enhanced proliferative activity and maintain long-term cell proliferation, which can be reversed by FLP recombinase. The piMEFs express most MEF markers and retain multipotency as they can differentiate into osteogenic, chondrogenic and adipogenic lineages upon BMP9 stimulation in vitro. Stem cell implantation studies indicate that piMEFs can form bone, cartilage and adipose tissues upon BMP9 stimulation, whereas FLP-mediated removal of SV40 T antigen diminishes the ability of piMEFs to differentiate into these lineages, possibly due to the reduced expansion of progenitor populations. Our results demonstrate that piggyBac transposon-mediated expression of SV40 T can effectively immortalize MEFs and that the reversibly immortalized piMEFs not only maintain long-term cell proliferation but also retain their multipotency. Thus, the high transposition efficiency and the potential footprint-free natures may render piggyBac transposition an effective and safe strategy to immortalize progenitor cells isolated from limited tissue supplies, which is essential for basic and translational studies. PMID:24845466

  3. A Universal Vector for High-Efficiency Multi-Fragment Recombineering of BACs and Knock-In Constructs

    PubMed Central

    Miller-Hodges, Eve; Slight, Joan; Thornburn, Anna; Devenney, Paul S.; Hohenstein, Peter

    2013-01-01

    There is an increasing need for more efficient generation of transgenic constructs. Here we present a universal multi-site Gateway vector for use in recombineering reactions. Using transgenic mouse models, we show its use for the generation of BAC transgenics and targeting vectors. The modular nature of the vector allows for rapid modification of constructs to generate different versions of the same construct. As such it will help streamline the generation of series of related transgenic models. PMID:23637962

  4. Driving Performance on the Descending Limb of Blood Alcohol Concentration (BAC) in Undergraduate Students: A Pilot Study

    PubMed Central

    Silvey, Dustin; Behm, David; Albert, Wayne J.

    2015-01-01

    Young drivers are overrepresented in collisions resulting in fatalities. It is not uncommon for young drivers to socially binge drink and decide to drive a vehicle a few hours after consumption. To better understand the risks that may be associated with this behaviour, the present study has examined the effects of a social drinking bout followed by a simulated drive in undergraduate students on the descending limb of their BAC (blood alcohol concentration) curve. Two groups of eight undergraduate students (n = 16) took part in this study. Participants in the alcohol group were assessed before drinking, then at moderate and low BAC as well as 24 hours post-acute consumption. This group consumed an average of 5.3 ± 1.4 (mean ± SD) drinks in an hour in a social context and were then submitted to a driving and a predicted crash risk assessment. The control group was assessed at the same time points without alcohol intake or social context.; at 8 a.m., noon, 3 p.m. and 8 a.m. the next morning. These multiple time points were used to measure any potential learning effects from the assessment tools (i.e. driving simulator and useful field of view test (UFOV)). Diminished driving performance at moderate BAC was observed with no increases in predicted crash risk. Moderate correlations between driving variables were observed. No association exists between driving variables and UFOV variables. The control group improved measures of selective attention after the third asessement. No learning effect was observed from multiple sessions with the driving simulator. Our results show that a moderate BAC, although legal, increases the risky behaviour. Effects of alcohol expectancy could have been displayed by the experimental group. UFOV measures and predicted crash risk categories were not sentitive enough to predict crash risk for young drivers, even when intoxicated. PMID:25723618

  5. Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1

    SciTech Connect

    Malouli, Daniel; Nakayasu, Ernesto S.; Viswanathan, Kasinath; Camp, David G.; Chang, W. L.; Barry, Peter A.; Smith, Richard D.; Fruh, Klaus

    2012-09-01

    Cytomegaloviruses are highly host restricted resulting in co-speciation with their hosts. As a natural pathogen of rhesus macaques (RM), Rhesus Cytomegalovirus (RhCMV) has therefore emerged as a highly relevant experimental model for pathogenesis and vaccine development due to its close evolutionary relationship to human CMV (HCMV). To date, most in vivo experiments performed with RhCMV employed strain 68-1 cloned as bacterial artificial chromosome (BAC). However, the complete genome sequence of the 68-1 BAC has not been determined. Furthermore, the gene content of the RhCMV genome is unknown and previous open reading frame (ORF) predictions relied solely on uninterrupted ORFs with an arbitrary cutoff of 300bp. To obtain a more precise picture of the actual proteins encoded by the most commonly used molecular clone of RhCMV we re-evaluated the RhCMV 68-1 BAC-genome by whole genome shotgun sequencing and determined the protein content of the resulting RhCMV virions by proteomics. By additionally comparing the RhCMV genome to that of several closely related Old World Monkey (OWM) CMVs we were able to filter out many unlikely ORFs and obtain a simplified map of the RhCMV genome. This comparative genomics analysis eliminated many genes previously characterized as RhCMV-specific while consolidating a high conservation of ORFs among OWM-CMVs and between RhCMV and HCMV. Moreover, virion proteomics independently validated the revised ORF predictions since only proteins encoded by predicted ORFs could be detected. Taken together these data suggest a much higher conservation of genome and virion structure between CMVs of humans, apes and OWMs than previously assumed. Remarkably, BAC-derived RhCMV is able to establish and maintain persistent infection despite the lack of multiple genes homologous to HCMV genes involved in tissue tropism.

  6. Human Bacterial Artificial Chromosome (BAC) Transgenesis Fully Rescues Noradrenergic Function in Dopamine β-Hydroxylase Knockout Mice.

    PubMed

    Cubells, Joseph F; Schroeder, Jason P; Barrie, Elizabeth S; Manvich, Daniel F; Sadee, Wolfgang; Berg, Tiina; Mercer, Kristina; Stowe, Taylor A; Liles, L Cameron; Squires, Katherine E; Mezher, Andrew; Curtin, Patrick; Perdomo, Dannie L; Szot, Patricia; Weinshenker, David

    2016-01-01

    Dopamine β-hydroxylase (DBH) converts dopamine (DA) to norepinephrine (NE) in noradrenergic/adrenergic cells. DBH deficiency prevents NE production and causes sympathetic failure, hypotension and ptosis in humans and mice; DBH knockout (Dbh -/-) mice reveal other NE deficiency phenotypes including embryonic lethality, delayed growth, and behavioral defects. Furthermore, a single nucleotide polymorphism (SNP) in the human DBH gene promoter (-970C>T; rs1611115) is associated with variation in serum DBH activity and with several neurological- and neuropsychiatric-related disorders, although its impact on DBH expression is controversial. Phenotypes associated with DBH deficiency are typically treated with L-3,4-dihydroxyphenylserine (DOPS), which can be converted to NE by aromatic acid decarboxylase (AADC) in the absence of DBH. In this study, we generated transgenic mice carrying a human bacterial artificial chromosome (BAC) encompassing the DBH coding locus as well as ~45 kb of upstream and ~107 kb of downstream sequence to address two issues. First, we characterized the neuroanatomical, neurochemical, physiological, and behavioral transgenic rescue of DBH deficiency by crossing the BAC onto a Dbh -/- background. Second, we compared human DBH mRNA abundance between transgenic lines carrying either a "C" or a "T" at position -970. The BAC transgene drove human DBH mRNA expression in a pattern indistinguishable from the endogenous gene, restored normal catecholamine levels to the peripheral organs and brain of Dbh -/- mice, and fully rescued embryonic lethality, delayed growth, ptosis, reduced exploratory activity, and seizure susceptibility. In some cases, transgenic rescue was superior to DOPS. However, allelic variation at the rs1611115 SNP had no impact on mRNA levels in any tissue. These results indicate that the human BAC contains all of the genetic information required for tissue-specific, functional expression of DBH and can rescue all measured Dbh deficiency

  7. Human Bacterial Artificial Chromosome (BAC) Transgenesis Fully Rescues Noradrenergic Function in Dopamine β-Hydroxylase Knockout Mice

    PubMed Central

    Cubells, Joseph F.; Schroeder, Jason P.; Barrie, Elizabeth S.; Manvich, Daniel F.; Sadee, Wolfgang; Berg, Tiina; Mercer, Kristina; Stowe, Taylor A.; Liles, L. Cameron; Squires, Katherine E.; Mezher, Andrew; Curtin, Patrick; Perdomo, Dannie L.; Szot, Patricia; Weinshenker, David

    2016-01-01

    Dopamine β-hydroxylase (DBH) converts dopamine (DA) to norepinephrine (NE) in noradrenergic/adrenergic cells. DBH deficiency prevents NE production and causes sympathetic failure, hypotension and ptosis in humans and mice; DBH knockout (Dbh -/-) mice reveal other NE deficiency phenotypes including embryonic lethality, delayed growth, and behavioral defects. Furthermore, a single nucleotide polymorphism (SNP) in the human DBH gene promoter (-970C>T; rs1611115) is associated with variation in serum DBH activity and with several neurological- and neuropsychiatric-related disorders, although its impact on DBH expression is controversial. Phenotypes associated with DBH deficiency are typically treated with L-3,4-dihydroxyphenylserine (DOPS), which can be converted to NE by aromatic acid decarboxylase (AADC) in the absence of DBH. In this study, we generated transgenic mice carrying a human bacterial artificial chromosome (BAC) encompassing the DBH coding locus as well as ~45 kb of upstream and ~107 kb of downstream sequence to address two issues. First, we characterized the neuroanatomical, neurochemical, physiological, and behavioral transgenic rescue of DBH deficiency by crossing the BAC onto a Dbh -/- background. Second, we compared human DBH mRNA abundance between transgenic lines carrying either a “C” or a “T” at position -970. The BAC transgene drove human DBH mRNA expression in a pattern indistinguishable from the endogenous gene, restored normal catecholamine levels to the peripheral organs and brain of Dbh -/- mice, and fully rescued embryonic lethality, delayed growth, ptosis, reduced exploratory activity, and seizure susceptibility. In some cases, transgenic rescue was superior to DOPS. However, allelic variation at the rs1611115 SNP had no impact on mRNA levels in any tissue. These results indicate that the human BAC contains all of the genetic information required for tissue-specific, functional expression of DBH and can rescue all measured Dbh

  8. BAC transgenic zebrafish reveal hypothalamic enhancer activity around obesity associated SNP rs9939609 within the human FTO gene.

    PubMed

    Rinkwitz, Silke; Geng, Fan-Suo; Manning, Elizabeth; Suster, Maximiliano; Kawakami, Koichi; Becker, Thomas S

    2015-10-01

    Single Nucleotide Polymorphisms in FTO intron 1 have been associated with obesity risk, leading to the hypothesis that FTO is the obesity-related gene. However, other studies have shown that the FTO gene is part of the regulatory domain of the neighboring IRX3 gene and that enhancers in FTO intron 1 regulate IRX3. While Irx3 activity was shown to be necessary in the hypothalamus for the metabolic function of Irx3 in mouse, no enhancers with hypothalamic activity have been demonstrated in the risk-associated region within FTO. In order to identify potential enhancers at the human FTO locus in vivo, we tested regulatory activity in FTO intron 1 using BAC transgenesis in zebrafish. A minimal gata2 promoter-GFP cassette was inserted 1.3 kb upstream of the obesity associated SNP rs9939609 in a human FTO BAC plasmid. In addition to the previously identified expression domains in notochord and kidney, human FTO BAC:GFP transgenic zebrafish larvae expressed GFP in the ventral posterior tuberculum, the posterior hypothalamus and the anterior brainstem, which are also expression domains of zebrafish irx3a. In contrast, an in-frame insertion of a GFP cassette at the FTO start codon resulted in weak ubiquitous GFP expression indicating that the promoter of FTO does likely not react to enhancers located in the obesity risk-associated region. PMID:26271004

  9. A nucleolus-predominant piggyBac transposase, NP-mPB, mediates elevated transposition efficiency in mammalian cells.

    PubMed

    Hong, Jin-Bon; Chou, Fu-Ju; Ku, Amy T; Fan, Hsiang-Hsuan; Lee, Tung-Lung; Huang, Yung-Hsin; Yang, Tsung-Lin; Su, I-Chang; Yu, I-Shing; Lin, Shu-Wha; Chien, Chung-Liang; Ho, Hong-Nerng; Chen, You-Tzung

    2014-01-01

    PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase) codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP) signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB). Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3-4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells. PMID:24586748

  10. A Nucleolus-Predominant piggyBac Transposase, NP-mPB, Mediates Elevated Transposition Efficiency in Mammalian Cells

    PubMed Central

    Ku, Amy T.; Fan, Hsiang-Hsuan; Lee, Tung-Lung; Huang, Yung-Hsin; Yang, Tsung-Lin; Su, I-Chang; Yu, I-Shing; Lin, Shu-Wha; Chien, Chung-Liang; Ho, Hong-Nerng; Chen, You-Tzung

    2014-01-01

    PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase) codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP) signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB). Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3–4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells. PMID:24586748

  11. Isolation and mode of action of bacteriocin BacC1 produced by nonpathogenic Enterococcus faecium C1.

    PubMed

    Goh, H F; Philip, K

    2015-08-01

    Lactic acid bacteria are present in fermented food products and help to improve shelf life and enhance the flavor of the food. They also produce metabolites such as bacteriocins to prevent the growth of undesirable or pathogenic bacteria. In this study, Enterococcus faecium C1 isolated from fermented cow milk was able to produce bacteriocin BacC1 and inhibit the growth of selected food-spoilage bacteria. The bacteriocin was purified through 4 steps: ammonium sulfate precipitation, hydrophobic interaction column, a series of centrifugal steps, and finally reversed-phase HPLC. A membrane permeability test using SYTOX green dye (Invitrogen, Grand Island, NY) showed that the bacteriocin caused significant disruptions to the test bacterial membrane, as shown by transmission electron microscopy. The molecular weight of the BacC1 obtained from SDS-PAGE was around 10kDa, and N-terminal sequencing revealed a partial amino acid sequence of BacC1: GPXGPXGP. The bacterial strain was nonhemolytic and not antibiotic resistant. Therefore, it has high potential for application in the food industry as an antimicrobial agent to extend the shelf life of food products. PMID:26004828

  12. Optimization of the piggyBac Transposon Using mRNA and Insulators: Toward a More Reliable Gene Delivery System

    PubMed Central

    Bire, Solenne; Ley, Déborah; Casteret, Sophie; Mermod, Nicolas; Bigot, Yves; Rouleux-Bonnin, Florence

    2013-01-01

    Integrating and expressing stably a transgene into the cellular genome remain major challenges for gene-based therapies and for bioproduction purposes. While transposon vectors mediate efficient transgene integration, expression may be limited by epigenetic silencing, and persistent transposase expression may mediate multiple transposition cycles. Here, we evaluated the delivery of the piggyBac transposase messenger RNA combined with genetically insulated transposons to isolate the transgene from neighboring regulatory elements and stabilize expression. A comparison of piggyBac transposase expression from messenger RNA and DNA vectors was carried out in terms of expression levels, transposition efficiency, transgene expression and genotoxic effects, in order to calibrate and secure the transposition-based delivery system. Messenger RNA reduced the persistence of the transposase to a narrow window, thus decreasing side effects such as superfluous genomic DNA cleavage. Both the CTF/NF1 and the D4Z4 insulators were found to mediate more efficient expression from a few transposition events. We conclude that the use of engineered piggyBac transposase mRNA and insulated transposons offer promising ways of improving the quality of the integration process and sustaining the expression of transposon vectors. PMID:24312663

  13. Validation of the BacT/ALERT(R) 3D System for Rapid Sterility Testing of Biopharmaceutical Samples.

    PubMed

    Jimenez, Luis; Rana, Narendra; Amalraj, Joseph; Walker, Kimberly; Travers, Kasey

    2012-01-01

    The BacT/ALERT® 3D system was validated to determine the sterility of different types of biopharmaceutical samples such as water for injection, unprocessed bulk, and finished bulk. The installation, operation, and performance qualification were completed and verified under good manufacturing practices. During the installation and operation validation stages, the functionality and security of the system and software were completed and verified. For the performance qualification, 11 microorganisms were evaluated, six compendial (Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus subtilis, Candida albicans, Aspergillus niger, Clostridium sporogenes), one representing the number one microbial species in sterile product recalls (Burkholderia cepacia), and four environmental isolates (Kocuria rhizophila, Staphylococcus haemolyticus, Methylobacterium radiotolerans, and Penicillium spp.). Nine of the microorganisms were spiked into three different types of biopharmaceutical samples by three different analysts on different days to ascertain the equivalence, ruggedness, sensitivity, time of detection, and repeatability. In all samples, the BacT/ALERT® exhibited equivalent or better detection than the standard test. With the exception of M. radiotolerans, all 11 microorganisms were detected within 2.5 days using the BacT/ALERT® system and the standard test. The detection times for M. radiotolerans in the three sample types averaged 5.77 days. The minimum detectable level of cells for all the microorganisms tested was found to be within 1 to 2 CFU. The system optimized sterility testing by the simultaneous on-line, non-destructive incubation and detection of microbial growth. PMID:22307661

  14. Public Libraries Section. Libraries Serving General Public Division. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    Papers on public libraries, which were presented at the 1983 International Federation of Library Associations (IFLA) conference, include: (1) "The Role of Public Libraries in Developing Countries with Particular Reference to the Gambia" by Sally P. C. N'Jie (The Gambia); (2) "Public Libraries in the Federal Republic of Germany (FRG)" by Friedrich…

  15. Dimensions of Public Library Effectiveness II: Library Performance.

    ERIC Educational Resources Information Center

    Van House, Nancy A.; Childers, Thomas

    1990-01-01

    Describes the Public Library Effectiveness Study (PLES), which was designed to apply models and methods of organizational effectiveness research to public libraries. Indicators of public library effectiveness are described, factor analysis results are presented, implications for evaluating library performance are discussed, and further research is…

  16. Automated Library Systems in ARL Libraries. SPEC Kit 126.

    ERIC Educational Resources Information Center

    Hirshon, Arnold

    Based on telephone interviews with 12 Association of Research Libraries (ARL) member libraries, this report presents the underlying reasons for the libraries' decisions relating to the design and implementation of automated library systems. The survey results are summarized, a list of respondents is provided, and profiles of present and planned…

  17. 2010 Library of the Year: Columbus Metropolitan Library

    ERIC Educational Resources Information Center

    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 operates…

  18. Whitmore Library: A New Concept of Public Library Services.

    ERIC Educational Resources Information Center

    Schuurman, Guy

    Until 1972, library services in Salt Lake County consisted of a group of branch libraries with nearly identical collections for recreational reading. Because the needs of the community had become more complex, a new regional library was built to coordinate library operations and establish new services. Among the innovations in public library…

  19. Library Statistics Program: State Library Agency Report for FY 2006

    ERIC Educational Resources Information Center

    Institute of Museum and Library Services, 2007

    2007-01-01

    This report marks the first release of library statistics data from the Institute of Museum and Library Services. It contains data on state library agencies in the 50 states and the District of Columbia for state fiscal year (FY) 2006. The data were collected through the State Library Agencies (StLA) Survey, the product of a cooperative effort…

  20. National Libraries Section. General Research Libraries Division. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    Papers on national library services and activities, which were presented at the 1983 International Federation of Library Associations (IFLA) conference, include: (1) "The National Library of China in its Gradual Application of Modern Technology," a discussion by Zhu Nan and Zhu Yan (China) of microform usage and library automation; (2) "The…

  1. The USF Libraries Virtual Library Project: A Blueprint for Development.

    ERIC Educational Resources Information Center

    Metz-Wiseman, Monica; Silver, Susan; Hanson, Ardis; Johnston, Judy; Grohs, Kim; Neville, Tina; Sanchez, Ed; Gray, Carolyn

    This report of the Virtual Library Planning Committee (VLPC) is intending to serve as a blueprint for the University of South Florida (USF) Libraries as it shifts from print to digital formats in its evolution into a "Virtual Library". A comprehensive planning process is essential for the USF Libraries to make optimum use of technology, fulfill…

  2. Simple piggyBac transposon-based mammalian cell expression system for inducible protein production

    PubMed Central

    Li, Zhijie; Michael, Iacovos P.; Zhou, Dongxia; Nagy, Andras; Rini, James M.

    2013-01-01

    Reported here is a piggyBac transposon-based expression system for the generation of doxycycline-inducible, stably transfected mammalian cell cultures for large-scale protein production. The system works with commonly used adherent and suspension-adapted mammalian cell lines and requires only a single transfection step. Moreover, the high uniform expression levels observed among clones allow for the use of stable bulk cell cultures, thereby eliminating time-consuming cloning steps. Under continuous doxycycline induction, protein expression levels have been shown to be stable for at least 2 mo in the absence of drug selection. The high efficiency of the system also allows for the generation of stable bulk cell cultures in 96-well format, a capability leading to the possibility of generating stable cell cultures for entire families of membrane or secreted proteins. Finally, we demonstrate the utility of the system through the large-scale production (140–750 mg scale) of an endoplasmic reticulum-resident fucosyltransferase and two potential anticancer protein therapeutic agents. PMID:23476064

  3. A first generation BAC-based physical map of the channel catfish genome

    PubMed Central

    Quiniou, Sylvie M-A; Waldbieser, Geoffrey C; Duke, Mary V

    2007-01-01

    Background Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL) and the effective positional cloning of genes. Results A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF) of 46,548 Bacterial Artificial Chromosomes (BAC) clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1) anchoring 19 of the largest contigs to the microsatellite linkage map 2) comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP) patterns seen in Southern blots, and 3) contig sequencing. Conclusion This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits. PMID:17284319

  4. A Sensitized PiggyBac-Based Screen for Regulators of Border Cell Migration in Drosophila

    PubMed Central

    Mathieu, Juliette; Sung, Hsin-Ho; Pugieux, Céline; Soetaert, Jan; Rorth, Pernille

    2007-01-01

    Migration of border cells during Drosophila melanogaster oogenesis is a good model system for investigating the genetic requirements for cell migration in vivo. We present a sensitized loss-of-function screen used to identify new genes required in border cells for their migration. Chromosomes bearing FRTs on all four major autosomal arms were mutagenized by insertions of the transposable element PiggyBac, allowing multiple parallel clonal screens and easy identification of the mutated gene. For border cells, we analyzed homozygous mutant clones positively marked with lacZ and sensitized by expression of dominant-negative PVR, the guidance receptor. We identified new alleles of genes already known to be required for border cell migration, including aop/yan, DIAP1, and taiman as well as a conserved Slbo-regulated enhancer downstream of shg/DE–cadherin. Mutations in genes not previously described to be required in border cells were also uncovered: hrp48, vir, rme-8, kismet, and puckered. puckered was unique in that the migration defects were observed only when PVR signaling was reduced. We present evidence that an excess of JNK signaling is deleterious for migration in the absence of PVR activity at least in part through Fos transcriptional activity and possibly through antagonistic effects on DIAP1. PMID:17483425

  5. [Integration sites and their characteristic analysis of piggyBac transposon in cattle genome].

    PubMed

    Du, Xin-Hua; Gao, Xue; Zhang, Lu-Pei; Gao, Hui-Jiang; Li, Jun-Ya; Xu, Shang-Zhong

    2013-06-01

    As a useful tool for genetic engineering, piggyBac (PB) transposons have been widely used in more than one species of transgenosis or generating mutation studies. At present, the studies about PB transposons in cattle were few. In order to get the PB transposon integration sites and summarize its characteristics in bovine genome, donor plasmid of PB[CMV-EGFP] and helper-dependent plasmid of pcDNA-PBase were constructed and transferred into bovine fibroblasts by Amaxa basic nucleofector kit for primary mammalian fibroblasts. Cell clones stably transfected were obtained after screening by G-418. Genomic DNA of transgenic cells was extracted and the integration sites of PB transposon were detected by genome walking technology. Eight integration sites were obtained in bovine genome, although only 5 sites were mapped on chromosomes 1, 2, 11, and X chromosome. We found that PB transposon was inserted into the "TTAA" location and integrated into the intergenic non-regulatory sites between two genes. Analysis of the composition of the five bases, which was close to the side of the PB integration sites "TTAA", showed that PB 5' tended to be inserted into region rich in GC (62.5%). From the study, we got that transposition occurred in cattle genome by PB transposons and the integration site information acquired from the research will provide theoretical references for bovine study by PB transposon. PMID:23774022

  6. Efficient Production of Fluorescent Transgenic Rats using the piggyBac Transposon.

    PubMed

    Li, Tianda; Shuai, Ling; Mao, Junjie; Wang, Xuepeng; Wang, Mei; Zhang, Xinxin; Wang, Leyun; Li, Yanni; Li, Wei; Zhou, Qi

    2016-01-01

    Rats with fluorescent markers are of great value for studies that trace lineage-specific development, particularly those assessing the differentiation potential of embryonic stem cells (ESCs). The piggyBac (PB) transposon is widely used for the efficient introduction of genetic modifications into genomes, and has already been successfully used to produce transgenic mice and rats. Here, we generated transgenic rats carrying either the desRed fluorescent protein (RFP) gene or the enhanced green fluorescent protein (eGFP) gene by injecting pronuclei with PB plasmids. We showed that the transgenic rats expressed the RFP or eGFP gene in many organs and had the capability to transmit the marker gene to the next generation through germline integration. In addition, rat embryonic stem cells (ESCs) carrying an RFP reporter gene can be derived from the blastocysts of the transgenic rats. Moreover, the RFP gene can be detected in chimeras derived from RFP ESCs via blastocyst injection. This work suggests that PB-mediated transgenesis is a powerful tool to generate transgenic rats expressing fluorescent proteins with high efficiency, and this technique can be used to derive rat ESCs expressing a reporter protein. PMID:27624004

  7. PiggyBac as a novel vector in cancer gene therapy: current perspective.

    PubMed

    Mirzaei, H; Sahebkar, A; Jaafari, M R; Hadjati, J; Javanmard, S H; Mirzaei, H R; Salehi, R

    2016-02-01

    Selection of suitable delivery system is one of the crucial aspects in gene therapy that determines the efficiency of gene therapy. The past two decades have witnessed extensive efforts for finding safe and efficient vectors to overcome the limitations of viral vectors. The utilization of DNA transposon-based vectors for gene therapy has emerged as a promising non-viral alternative. DNA 'cut-and-paste' is one of the main mechanisms of genome engineering by transposon elements. However, the lack of an efficient transposition system has limited the utilization of transposon vectors in mice and mammalian systems. PiggyBac (PB) is known as a highly efficient DNA transposon originally isolated from Trichoplusia ni as an alternative to Sleeping Beauty (SB). It has been shown that PB can be functional in various species including mammalian systems. This vector could overcome some limitations of other vectors in cancer gene therapy. Some advantages of PB include the capacity for integration into the genome and providing a stable expression, capacity to harbor 10 and 9.1 kb of foreign DNA into the host genome, without a significant reduction in their transposition activity and display non-overlapping targeting preferences. However, to advance PB to clinical applications, some obstacles still require to be overcome to improve its safety and efficiency. Hence, it seems that this vector could open new horizons in gene and cancer therapy. PMID:26742580

  8. Chimeric piggyBac transposases for genomic targeting in human cells.

    PubMed

    Owens, Jesse B; Urschitz, Johann; Stoytchev, Ilko; Dang, Nong C; Stoytcheva, Zoia; Belcaid, Mahdi; Maragathavally, Kommineni J; Coates, Craig J; Segal, David J; Moisyadi, Stefan

    2012-08-01

    Integrating vectors such as viruses and transposons insert transgenes semi-randomly and can potentially disrupt or deregulate genes. For these techniques to be of therapeutic value, a method for controlling the precise location of insertion is required. The piggyBac (PB) transposase is an efficient gene transfer vector active in a variety of cell types and proven to be amenable to modification. Here we present the design and validation of chimeric PB proteins fused to the Gal4 DNA binding domain with the ability to target transgenes to pre-determined sites. Upstream activating sequence (UAS) Gal4 recognition sites harbored on recipient plasmids were preferentially targeted by the chimeric Gal4-PB transposase in human cells. To analyze the ability of these PB fusion proteins to target chromosomal locations, UAS sites were randomly integrated throughout the genome using the Sleeping Beauty transposon. Both N- and C-terminal Gal4-PB fusion proteins but not native PB were capable of targeting transposition nearby these introduced sites. A genome-wide integration analysis revealed the ability of our fusion constructs to bias 24% of integrations near endogenous Gal4 recognition sequences. This work provides a powerful approach to enhance the properties of the PB system for applications such as genetic engineering and gene therapy. PMID:22492708

  9. A piggyBac insertion disrupts Foxl2 expression that mimics BPES syndrome in mice.

    PubMed

    Shi, Fubiao; Ding, Sheng; Zhao, Shimin; Han, Min; Zhuang, Yuan; Xu, Tian; Wu, Xiaohui

    2014-07-15

    Blepharophimosis, ptosis, epicanthus inversus syndrome (BPES) is an autosomal dominant genetic disorder characterized by small palpebral fissures and other craniofacial malformations, often with (type I) but could also without (type II) premature ovarian failure. While mutations of the forkhead transcription factor FOXL2 are associated with and likely be responsible for many BPES cases, how FOXL2 affects craniofacial development remain to be understood. Through a large-scale piggyBac (PB) insertion mutagenesis, we have identified a mouse mutant carrying a PB insertion ∼160 kb upstream of the transcription start site (TSS) of Foxl2. The insertion reduces, but not eliminates, the expression of Foxl2. This mutant, but not its revertant, displays BPES-like conditions such as midface hypoplasia, eyelid abnormalities and female subfertility. Further analysis indicates that the mutation does not affect mandible, but causes premature fusion of the premaxilla-maxilla suture, smaller premaxilla and malformed maxilla during midface development. We further identified an evolutionarily conserved fragment near the insertion site and observed enhancer activity of this element in tissue culture cells. Analyses using DNase I hypersensitivity assay and chromosome conformation capture assay in developing maxillary and periocular tissues suggest that the DNA region near the insertion site likely interacts with Foxl2 TSS. Therefore, this mutant presents an excellent animal model for mechanistic study of BPES and regulation of Foxl2. PMID:24565867

  10. piggyBac transposons expressing full-length human dystrophin enable genetic correction of dystrophic mesoangioblasts

    PubMed Central

    Loperfido, Mariana; Jarmin, Susan; Dastidar, Sumitava; Di Matteo, Mario; Perini, Ilaria; Moore, Marc; Nair, Nisha; Samara-Kuko, Ermira; Athanasopoulos, Takis; Tedesco, Francesco Saverio; Dickson, George; Sampaolesi, Maurilio; VandenDriessche, Thierry; Chuah, Marinee K.

    2016-01-01

    Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disorder caused by the absence of dystrophin. We developed a novel gene therapy approach based on the use of the piggyBac (PB) transposon system to deliver the coding DNA sequence (CDS) of either full-length human dystrophin (DYS: 11.1 kb) or truncated microdystrophins (MD1: 3.6 kb; MD2: 4 kb). PB transposons encoding microdystrophins were transfected in C2C12 myoblasts, yielding 65±2% MD1 and 66±2% MD2 expression in differentiated multinucleated myotubes. A hyperactive PB (hyPB) transposase was then deployed to enable transposition of the large-size PB transposon (17 kb) encoding the full-length DYS and green fluorescence protein (GFP). Stable GFP expression attaining 78±3% could be achieved in the C2C12 myoblasts that had undergone transposition. Western blot analysis demonstrated expression of the full-length human DYS protein in myotubes. Subsequently, dystrophic mesoangioblasts from a Golden Retriever muscular dystrophy dog were transfected with the large-size PB transposon resulting in 50±5% GFP-expressing cells after stable transposition. This was consistent with correction of the differentiated dystrophic mesoangioblasts following expression of full-length human DYS. These results pave the way toward a novel non-viral gene therapy approach for DMD using PB transposons underscoring their potential to deliver large therapeutic genes. PMID:26682797

  11. Highly efficient integration and expression of piggyBac-derived cassettes in the honeybee (Apis mellifera)

    PubMed Central

    Schulte, Christina; Theilenberg, Eva; Müller-Borg, Marion; Gempe, Tanja; Beye, Martin

    2014-01-01

    Honeybees (Apis mellifera), which are important pollinators of plants, display remarkable individual behaviors that collectively contribute to the organization of a complex society. Advances in dissecting the complex processes of honeybee behavior have been limited in the recent past due to a lack of genetic manipulation tools. These tools are difficult to apply in honeybees because the unit of reproduction is the colony, and many interesting phenotypes are developmentally specified at later stages. Here, we report highly efficient integration and expression of piggyBac-derived cassettes in the honeybee. We demonstrate that 27 and 20% of queens stably transmitted two different expression cassettes to their offspring, which is a 6- to 30-fold increase in efficiency compared with those generally reported in other insect species. This high efficiency implies that an average beekeeping facility with a limited number of colonies can apply this tool. We demonstrated that the cassette stably and efficiently expressed marker genes in progeny under either an artificial or an endogenous promoter. This evidence of efficient expression encourages the use of this system to inhibit gene functions through RNAi in specific tissues and developmental stages by using various promoters. We also showed that the transgenic marker could be used to select transgenic offspring to be employed to facilitate the building of transgenic colonies via the haploid males. We present here the first to our knowledge genetic engineering tool that will efficiently allow for the systematic detection and better understanding of processes underlying the biology of honeybees. PMID:24821811

  12. piggyBac transposons expressing full-length human dystrophin enable genetic correction of dystrophic mesoangioblasts.

    PubMed

    Loperfido, Mariana; Jarmin, Susan; Dastidar, Sumitava; Di Matteo, Mario; Perini, Ilaria; Moore, Marc; Nair, Nisha; Samara-Kuko, Ermira; Athanasopoulos, Takis; Tedesco, Francesco Saverio; Dickson, George; Sampaolesi, Maurilio; VandenDriessche, Thierry; Chuah, Marinee K

    2016-01-29

    Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disorder caused by the absence of dystrophin. We developed a novel gene therapy approach based on the use of the piggyBac (PB) transposon system to deliver the coding DNA sequence (CDS) of either full-length human dystrophin (DYS: 11.1 kb) or truncated microdystrophins (MD1: 3.6 kb; MD2: 4 kb). PB transposons encoding microdystrophins were transfected in C2C12 myoblasts, yielding 65±2% MD1 and 66±2% MD2 expression in differentiated multinucleated myotubes. A hyperactive PB (hyPB) transposase was then deployed to enable transposition of the large-size PB transposon (17 kb) encoding the full-length DYS and green fluorescence protein (GFP). Stable GFP expression attaining 78±3% could be achieved in the C2C12 myoblasts that had undergone transposition. Western blot analysis demonstrated expression of the full-length human DYS protein in myotubes. Subsequently, dystrophic mesoangioblasts from a Golden Retriever muscular dystrophy dog were transfected with the large-size PB transposon resulting in 50±5% GFP-expressing cells after stable transposition. This was consistent with correction of the differentiated dystrophic mesoangioblasts following expression of full-length human DYS. These results pave the way toward a novel non-viral gene therapy approach for DMD using PB transposons underscoring their potential to deliver large therapeutic genes. PMID:26682797

  13. [Thermal resistance of the spores of a Bac. stearothermophilus culture used for the preparation of bioindicators].

    PubMed

    Kalinina, N M; Shilova, S V; Motina, G L; Chaĭkovskaia, S M

    1982-02-01

    Thermostability of the spores of Bac. stearothermophilus in ampoules and capillaries in concentrations of 10(9), 10(8) and 10(6) cells per 1 ml of sodium chloride isotonic solution was determined at 119 to 124 degrees C with an interval of 1 degree C and an exposure time of 5, 10, 15, 20, 25, 30, 35 and 40 minutes. The results were used for plotting the survival curves. The time of the microbial death in the ampoules and capillaries at all the temperatures was the same and the ampoules were chosen as the bioindicator vehicle because of their availability and convenience in exploitation. The survival curves may be used for determination of the optimal sterilization conditions. The spore concentration of the thermostable culture in the bioindicator should be equal or exceed the level of the object microbial contamination. In the present study the concentration of the test microbe spores in the bioindicator was 10(6)--10(8) cells/ml. PMID:7065645

  14. C9orf72 BAC Transgenic Mice Display Typical Pathologic Features of ALS/FTD.

    PubMed

    O'Rourke, Jacqueline G; Bogdanik, Laurent; Muhammad, A K M G; Gendron, Tania F; Kim, Kevin J; Austin, Andrew; Cady, Janet; Liu, Elaine Y; Zarrow, Jonah; Grant, Sharday; Ho, Ritchie; Bell, Shaughn; Carmona, Sharon; Simpkinson, Megan; Lall, Deepti; Wu, Kathryn; Daughrity, Lillian; Dickson, Dennis W; Harms, Matthew B; Petrucelli, Leonard; Lee, Edward B; Lutz, Cathleen M; Baloh, Robert H

    2015-12-01

    Noncoding expansions of a hexanucleotide repeat (GGGGCC) in the C9orf72 gene are the most common cause of familial amyotrophic lateral sclerosis and frontotemporal dementia. Here we report transgenic mice carrying a bacterial artificial chromosome (BAC) containing the full human C9orf72 gene with either a normal allele (15 repeats) or disease-associated expansion (∼100-1,000 repeats; C9-BACexp). C9-BACexp mice displayed pathologic features seen in C9orf72 expansion patients, including widespread RNA foci and repeat-associated non-ATG (RAN) translated dipeptides, which were suppressed by antisense oligonucleotides targeting human C9orf72. Nucleolin distribution was altered, supporting that either C9orf72 transcripts or RAN dipeptides promote nucleolar dysfunction. Despite early and widespread production of RNA foci and RAN dipeptides in C9-BACexp mice, behavioral abnormalities and neurodegeneration were not observed even at advanced ages, supporting the hypothesis that RNA foci and RAN dipeptides occur presymptomatically and are not sufficient to drive neurodegeneration in mice at levels seen in patients. PMID:26637796

  15. Rapid recombinant protein production from piggyBac transposon-mediated stable CHO cell pools.

    PubMed

    Balasubramanian, Sowmya; Matasci, Mattia; Kadlecova, Zuzana; Baldi, Lucia; Hacker, David L; Wurm, Florian M

    2015-04-20

    Heterogeneous populations of stably transfected cells (cell pools) can serve for the rapid production of moderate amounts of recombinant proteins. Here, we propose the use of the piggyBac (PB) transposon system to improve the productivity and long-term stability of cell pools derived from Chinese hamster ovary (CHO) cells. PB is a naturally occurring genetic element that has been engineered to facilitate the integration of a transgene into the genome of the host cell. In this report PB-derived cell pools were generated after 10 days of selection with puromycin. The resulting cell pools had volumetric productivities that were 3-4 times higher than those achieved with cell pools generated by conventional plasmid transfection even though the number of integrated transgene copies per cell was similar in the two populations. In 14-day batch cultures, protein levels up to 600 and 800 mg/L were obtained for an Fc-fusion protein and a monoclonal antibody, respectively, at volumetric scales up to 1L. In general, the volumetric protein yield from cell pools remained constant for up to 3 months in the absence of selection. In conclusion, transfection of CHO cells with the PB transposon system is a simple, efficient, and reproducible approach to the generation of cell pools for the rapid production of recombinant proteins. PMID:25758242

  16. piggyBac-like elements in cotton bollworm, Helicoverpa armigera (Hübner).

    PubMed

    Sun, Z C; Wu, M; Miller, T A; Han, Z J

    2008-02-01

    Two piggyBac-like elements (PLEs) were identified in the cotton bollworm, Helicoverpa armigera, and were designated as HaPLE1 and HaPLE2. HaPLE1 is flanked by 16 bp inverted terminal repeats (ITRs) and the duplicated TTAA tetranucleotide, and contains an open reading frame (ORF) of 1794 bp with the presumed DDD domain, indicating that this element may be an active autonomously mobile element. HaPLE2 was found with the same ITRs, but lacks the majority of an ORF-encoding transposase. Thus, this element was thought to be a non-autonomous element. Transposable element displays and distribution of the two PLEs in individuals from three different H. armigera populations suggest that transmobilization of HaPLE2 by the transposase of HaPLE1 may be likely, and mobilization of HaPLE1 might occur not only within the same individual, but also among different individuals. In addition, horizontal transfer was probably involved in the evolution of PLEs between H. armigera and Trichoplusia ni. PMID:18237280

  17. N17 Modifies Mutant Huntingtin Nuclear Pathogenesis and Severity of Disease in HD BAC Transgenic Mice

    PubMed Central

    Gu, Xiaofeng; Cantle, Jeffrey P.; Greiner, Erin R.; Lee, C.Y. Daniel; Barth, Albert M.; Gao, Fuying; Park, Chang Sin; Zhang, Zhiqiang; Sandoval-Miller, Susana; Zhang, Richard L.; Diamond, Marc; Mody, Istvan; Coppola, Giovanni

    2015-01-01

    SUMMARY The nucleus is a critical subcellular compartment for the pathogenesis of polyglutamine disorders, including Huntington’s disease (HD). Recent studies suggest the first 17-amino-acid domain (N17) of mutant Huntingtin (mHTT) mediates its nuclear exclusion in cultured cells. Here, we test whether N17 could be a molecular determinant of nuclear mHTT pathogenesis in vivo. BAC transgenic mice expressing mHTT lacking the N17 domain (BACHD-ΔN17) show dramatically accelerated mHTT pathology exclusively in the nucleus, which is associated with HD-like transcriptionopathy. Interestingly, BACHD-ΔN17 mice manifest more overt disease-like phenotypes than the original BACHD mice, including body weight loss, movement deficits, robust striatal neuronal loss, and neuroinflammation. Mechanistically, N17 is necessary for nuclear exclusion of small mHTT fragments that are part of nuclear pathology in HD. Together, our study suggests that N17 modifies nuclear pathogenesis and disease severity in HD mice by regulating subcellular localization of known nuclear pathogenic mHTT species. PMID:25661181

  18. Libraries for genomic SELEX.

    PubMed Central

    Singer, B S; Shtatland, T; Brown, D; Gold, L

    1997-01-01

    An increasing number of proteins are being identified that regulate gene expression by binding specific nucleic acidsin vivo. A method termed genomic SELEX facilitates the rapid identification of networks of protein-nucleic acid interactions by identifying within the genomic sequences of an organism the highest affinity sites for any protein of the organism. As with its progenitor, SELEX of random-sequence nucleic acids, genomic SELEX involves iterative binding, partitioning, and amplification of nucleic acids. The two methods differ in that the variable region of the nucleic acid library for genomic SELEX is derived from the genome of an organism. We have used a quick and simple method to construct Escherichia coli, Saccharomyces cerevisiae, and human genomic DNA PCR libraries that can be transcribed with T7 RNA polymerase. We present evidence that the libraries contain overlapping inserts starting at most of the positions within the genome, making these libraries suitable for genomic SELEX. PMID:9016629

  19. Mainstreaming the New Library.

    ERIC Educational Resources Information Center

    Keeler, Elizabeth

    1982-01-01

    This discussion of methods of integrating the corporate library into the mainstream of affairs highlights three major elements of the process: marketing, production, and advertising. Professionalism and the information seeking behavior of clients are noted. Five references are provided. (EJS)

  20. Library for Nonlinear Optimization

    Energy Science and Technology Software Center (ESTSC)

    2001-10-09

    OPT++ is a C++ object-oriented library for nonlinear optimization. This incorporates an improved implementation of an existing capability and two new algorithmic capabilities based on existing journal articles and freely available software.

  1. Marketing the Library.

    ERIC Educational Resources Information Center

    Dragon, Andrea C.

    1979-01-01

    Describes the positive action using marketing strategies that libraries must take to capture their share of the post-Proposition 13 tax dollar. Strategies discussed relate to price, product, promotion, and place. (JD)

  2. Iranian Library Studies

    ERIC Educational Resources Information Center

    Harvey, John F.

    1973-01-01

    The development of library education in Iran is presented in some detail. In addition, the origins, purposes, operations and services of the Iranian Documentation Centre and the Tehran Book Processing Centre are described. (7 references) (KE)

  3. Increasing Public Library Productivity.

    ERIC Educational Resources Information Center

    Samuelson, Howard

    1981-01-01

    Suggests ways of improving productivity for public libraries faced with increased accountability, dwindling revenues, and continuing inflation. Techniques described include work simplification, work analysis, improved management, and employee motivation. (RAA)

  4. Large Spectral Library Problem

    SciTech Connect

    Chilton, Lawrence K.; Walsh, Stephen J.

    2008-10-03

    Hyperspectral imaging produces a spectrum or vector at each image pixel. These spectra can be used to identify materials present in the image. In some cases, spectral libraries representing atmospheric chemicals or ground materials are available. The challenge is to determine if any of the library chemicals or materials exist in the hyperspectral image. The number of spectra in these libraries can be very large, far exceeding the number of spectral channels collected in the ¯eld. Suppose an image pixel contains a mixture of p spectra from the library. Is it possible to uniquely identify these p spectra? We address this question in this paper and refer to it as the Large Spectral Library (LSL) problem. We show how to determine if unique identi¯cation is possible for any given library. We also show that if p is small compared to the number of spectral channels, it is very likely that unique identi¯cation is possible. We show that unique identi¯cation becomes less likely as p increases.

  5. NSUF Irradiated Materials Library

    SciTech Connect

    Cole, James Irvin

    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.

  6. Improved detection of bacterial growth in continuous ambulatory peritoneal dialysis effluent by use of BacT/Alert FAN bottles.

    PubMed Central

    Alfa, M J; Degagne, P; Olson, N; Harding, G K

    1997-01-01

    Culture-negative peritonitis is a major complication for patients on continuous ambulatory peritoneal dialysis (CAPD) and precludes organism-specific therapy. The aim of the present study was to compare inoculation of 10 ml of CAPD effluent into BacT/Alert blood culture bottles (FAN [fastidious antimicrobic neutralizing], BacTAlert aerobic [BTA], and BacT/Alert anaerobic [BTAn] bottles) to our conventional method of using 50 ml of concentrated CAPD effluent to inoculate peptone broth bottles (BD bottles) and MacConkey agar and blood agar medium (BA-MAC). The FAN, BTA, and BTAn bottles were monitored automatically in the BacT/Alert blood culture instrument. A total of 207 CAPD effluents were studied, and in 97 bacteria were detected by at least one method. Compared to BTA bottles (79 of 97; 81.4%), BTAn bottles (78 of 97; 80.4%), and BD bottles (88 of 97; 90.7%), the single best broth medium for detecting bacterial growth in CAPD effluents was the FAN bottle (90 of 97 effluents; 92.8%). A total of 125 bacterial species were detected by any method, and the majority (91.8%) of CAPD effluents were infected with a single species. A combination of FAN and BTAn bottles detected 111 of 125 (88.8%) of all organisms, whereas a combination of BD bottles and BA-MAC detected 107 of 125 (85.6%) of all organisms. One or more organisms that would have been completely missed by the conventional method with BD bottles and BA-MAC were detected in 18 CAPD effluents. Of these 18 CAPD effluents, 6 showed no growth by the conventional method with BD bottles and BA-MAC. On the basis of our data, the most sensitive and least labor intensive method was direct inoculation of 10 ml of CAPD effluent into a FAN bottle and a BTAn bottle, which could be automatically monitored by the BacT/Alert blood culture instrument. On the basis of case definitions for peritonitis, the sensitivities and specificities of the methods with FAN and BTAn bottles and with BD bottles and BA-MAC were 81.1 and 98

  7. IFLA General Conference, 1992. Division of General Research Libraries: Section on National Libraries; Section on Parliamentary Libraries; Section on University Libraries and Other General Research Libraries. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations and Institutions, London (England).

    Fifteen papers delivered for the Division of General Research Libraries at the 1992 International Federation of Library Associations and Institutions annual meeting are presented. These papers deal with national libraries, parliamentary (legislative) libraries, and university libraries. The papers are: (1) "Seeking Alternatives to National…

  8. Library Services Funding Assessment

    NASA Technical Reports Server (NTRS)

    Lorig, Jonathan A.

    2004-01-01

    The Glenn Technical Library is a science and engineering library that primarily supports research activities at the Glenn Research Center, and provides selected services to researchers at all of the NASA research centers. Resources available in the library include books, journals, CD-ROMs, and access to various online sources, as well as live reference and inter-library loan services. The collection contains over 77,000 books, 800,000 research reports, and print or online access to over 1,400 journals. Currently the library operates within the Logistics and Technical Information Division, and is funded as an open-access resource within the GRC. Some of the research units at the GRC have recently requested that the library convert to a "pay-for-services" model, in which individual research units could fund only those journal subscriptions for which they have a specific need. Under this model, the library would always maintain a certain minimum level of pooled-expense services, including the ready reference and book collections, and inter-library loan services. Theoretically the "pay-for-services" model would encourage efficient financial allocation, and minimize the extent to which paid journal subscriptions go unused. However, this model also could potentially negate the benefits of group purchases for journal subscriptions and access. All of the major journal publishers offer package subscriptions that compare favorably in cost with the sum of individual subscription costs for a similar selection of titles. Furthermore, some of these subscription packages are "consortium" purchases that are funded collectively by the libraries at multiple NASA research centers; such consortia1 memberships would be difficult for the library to pay, if enough GRC research units were to withdraw their pooled contributions. cost of collectively-funded journal access with the cost of individual subscriptions. My primary task this summer is to create the cost dataset framework, and

  9. Electronic Library: A TERI Experiment.

    ERIC Educational Resources Information Center

    Kar, Debal C.; Deb, Subrata; Kumar, Satish

    2003-01-01

    Discusses the development of Electronic Library at TERI (The Energy and Resources Institute, New Delhi). Highlights include: hardware and software used; the digital library/Virtual Electronic Library; directory of Internet journals; virtual reference resources; electronic collection/Physical Electronic Library; downloaded online full-length…

  10. Oklahoma Library Trustee Handbook, 1996.

    ERIC Educational Resources Information Center

    Oklahoma State Dept. of Libraries, Oklahoma City. Office of Library Development.

    Library board members are an integral part of public libraries. Because of the importance of their role, this handbook gives library trustees in Oklahoma a basic understanding of their responsibilities and power. It contains useful information about developing policy, the board/director relationship, funding, intellectual freedom, library laws,…

  11. Fundamentals of the Slide Library.

    ERIC Educational Resources Information Center

    Boerner, Susan Zee

    This paper is an introduction to the fundamentals of the art (including architecture) slide library, with some emphasis on basic procedures of the science slide library. Information in this paper is particularly relevant to the college, university, and museum slide library. Topics addressed include: (1) history of the slide library; (2) duties of…

  12. Standards for Health Sciences Libraries.

    ERIC Educational Resources Information Center

    Stinson, E. Ray

    1982-01-01

    Discusses service standards (level of excellence or adequacy in performance of library service) and their incorporation in the accreditation process for hospital library service and academic health sciences libraries. The certification program developed for health sciences librarians by the Medical Library Association is reviewed. Fifty-nine…

  13. Clarifying and Defining Library Services.

    ERIC Educational Resources Information Center

    Shubert, Joseph F., Ed.; Josey, E. J., Ed.

    1991-01-01

    This issue presents articles which, in some way, help to clarify and define library services. It is hoped that this clarification in library service will serve to secure the resources libraries need to serve the people of New York. The following articles are presented: (1) Introduction: "Clarifying and Defining Library Services" (Joseph F.…

  14. Library Guide for International Students.

    ERIC Educational Resources Information Center

    Rutgers, The State Univ., New Brunswick, NJ. Univ. Libraries.

    This guide to Rutgers University Libraries (RUL) is intended as an introduction to the library system for foreign students studying at the University. The guide consists of the following: welcoming remarks; a brief discussion of the American academic library systems; a list of the locations and abbreviations of the 25 libraries, collections and…

  15. Hispanic College Students Library Experience

    ERIC Educational Resources Information Center

    Lumley, Risa; Newman, Eric; Brown, Haakon T.

    2015-01-01

    This study looks at undergraduate Hispanic students' interpretations and current perceptions of the academic library's purpose, usefulness and value. What are the reasons to use the library? What are the barriers to use? This study will examine academic libraries' move toward electronic library materials and what it means for Hispanic students.…

  16. Rural Libraries and Community Development.

    ERIC Educational Resources Information Center

    Vavrek, Bernard

    1995-01-01

    Discusses the role of rural public libraries in the information age. Characteristics of rural communities that library planners should consider are conservatism, the lack of professionally trained librarians, library trustee involvement, the need for marketing, and gender balance. Suggestions for recreating rural libraries and providing…

  17. Security Issues of Academic Libraries.

    ERIC Educational Resources Information Center

    Lorenzen, Michael G.

    This study examines and evaluates security issues in academic libraries and examines how educators in institutions of higher learning deal with them. Security issues include: the theft of library materials, the mutilation or vandalism of library materials, dealing with deranged and/or disruptive patrons, and assaults on library patrons and staff.…

  18. Trends in Philippine Library History.

    ERIC Educational Resources Information Center

    Hernandez, Vicente S.

    This paper divides Philippine library history into three periods, establishing a relationship between historical events and library trends. During the Spanish period, modern library trends were introduced through the establishment of the Sociedad Economica in 1780, but did not influence Philippine library culture until the later part of the 19th…

  19. College Library Program. A Proposal.

    ERIC Educational Resources Information Center

    Kentucky Univ., Lexington. Univ. Libraries.

    A second draft of the University of Kentucky libraries proposal to the Council on Library Resources describes in detail how the grant would be used. A position of Library Service Coordinator is proposed, with librarian acting as liaison to the General Studies program. This would enable the library to contribute to undergraduate education, and…

  20. The Library Administrator's Automation Handbook.

    ERIC Educational Resources Information Center

    Boss, Richard W.

    One of the most significant decisions in a library administrator's career is the decision to automate one or more of a library's operations. This book describes the present state of local library automation; the planning, selection, and implementation process; and the library administrator's role in the process. The bulk of the text provides a…