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Sample records for gene library

  1. Making Your Own Gene Library.

    ERIC Educational Resources Information Center

    Perez-Ortin, Jose E.; Li Del Olmo, Marcel; Matallana, Emilia; Tordera, Vicente

    1997-01-01

    Presents an experiment aimed at constructing a genomic library that can be carried out over a week. Helps students learn concepts such as donor and vector DNAs, construction of recombinant DNA, host strain, and experiments in gene cloning more clearly. (PVD)

  2. Gene and library synthesis without amplification: polymerase step reaction (PSR).

    PubMed

    Lee, Zhuo-Bin; Firnhaber, Christopher; Clarke, Jesse; DeDecker, Brian S

    2015-09-01

    Current gene synthesis methods often incorporate a PCR amplification step in order to yield final material sufficient for resolution from multiple off-products. These amplification steps can cause stochastic sampling effects that propagate errors in gene synthesis or decrease variability when applied to the construction of randomized libraries. We have developed a simple DNA polymerase-based gene synthesis reaction, polymerase step reaction (PSR), that assembles DNA oligonucleotides in a unidirectional fashion without the need for amplification. We demonstrate that PSR is efficient, with little off-product production, no detectable error propagation, and maximized variability in the synthesis of a phage display library.

  3. Phenotypic mutant library: potential for gene discovery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid development of high throughput and affordable Next- Generation Sequencing (NGS) techniques has renewed interest in gene discovery using forward genetics. The conventional forward genetic approach starts with isolation of mutants with a phenotype of interest, mapping the mutation within a s...

  4. Rational design of orthogonal libraries of protein coding genes.

    PubMed

    Ryan, Daniel; Papamichail, Dimitris

    2013-05-17

    Array-based oligonucleotide synthesis technologies provide access to thousands of custom-designed sequence variants at low cost. Large-scale synthesis and high-throughput assays have become valuable experimental tools to study in detail the interplay between sequence and function. We have developed a methodology and corresponding algorithms for the design of diverse protein coding gene libraries, to exploit the potential of multiplex synthesis and help elucidate the effects of codon utilization and other factors in gene expression. Using our algorithm, we have computationally designed gene libraries with hundreds to thousands of orthogonal codon usage variants, uniformly exploring the design space of codon utilization, while demanding only a small fraction of the synthesis cost that would be required if these variants were synthesized independently.

  5. Gene enrichment in plant genomic shotgun libraries.

    PubMed

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

    2003-04-01

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

  6. Gene recovery microdissection (GRM) a process for producing chromosome region-specific libraries of expressed genes

    SciTech Connect

    Christian, A T; Coleman, M A; Tucker, J D

    2001-02-08

    Gene Recovery Microdissection (GRM) is a unique and cost-effective process for producing chromosome region-specific libraries of expressed genes. It accelerates the pace, reduces the cost, and extends the capabilities of functional genomic research, the means by which scientists will put to life-saving, life-enhancing use their knowledge of any plant or animal genome.

  7. 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…

  8. Comparison of inherently essential genes of Porphyromonas gingivalis identified in two transposon-sequencing libraries.

    PubMed

    Hutcherson, J A; Gogeneni, H; Yoder-Himes, D; Hendrickson, E L; Hackett, M; Whiteley, M; Lamont, R J; Scott, D A

    2016-08-01

    Porphyromonas gingivalis is a Gram-negative anaerobe and keystone periodontal pathogen. A mariner transposon insertion mutant library has recently been used to define 463 genes as putatively essential for the in vitro growth of P. gingivalis ATCC 33277 in planktonic culture (Library 1). We have independently generated a transposon insertion mutant library (Library 2) for the same P. gingivalis strain and herein compare genes that are putatively essential for in vitro growth in complex media, as defined by both libraries. In all, 281 genes (61%) identified by Library 1 were common to Library 2. Many of these common genes are involved in fundamentally important metabolic pathways, notably pyrimidine cycling as well as lipopolysaccharide, peptidoglycan, pantothenate and coenzyme A biosynthesis, and nicotinate and nicotinamide metabolism. Also in common are genes encoding heat-shock protein homologues, sigma factors, enzymes with proteolytic activity, and the majority of sec-related protein export genes. In addition to facilitating a better understanding of critical physiological processes, transposon-sequencing technology has the potential to identify novel strategies for the control of P. gingivalis infections. Those genes defined as essential by two independently generated TnSeq mutant libraries are likely to represent particularly attractive therapeutic targets.

  9. Engineering Complex Microbial Phenotypes with Continuous Genetic Integration and Plasmid Based Multi-Gene Library

    DTIC Science & Technology

    2010-01-01

    tetracycline reistance ) gene to integrate into the antibiotic resistance gene present in the parent strain library for the 3rd and 4th rounds of DNA...is used as a generic desirable trait to provide a proof of the concept). An antibiotic gene marker was inserted into the E. coli chromosome to be...used as a target for homologous integration of a second antibiotic gene marker along with ~ 3 kb L. pl DNA fragments. The second antibiotic gene

  10. A potato skin SSH library yields new candidate genes for suberin biosynthesis and periderm formation.

    PubMed

    Soler, Marçal; Serra, Olga; Fluch, Silvia; Molinas, Marisa; Figueras, Mercè

    2011-05-01

    Potato (Solanum tuberosum) tubers are underground storage organs covered by the skin or periderm, a suberized layer that protects inner flesh from dehydration and pathogens. Understanding the molecular processes associated with periderm formation is of great importance for a better knowledge of this protective tissue and for improving the storage life of tubers. Here, to isolate new candidate genes for potato periderm, a suppression subtractive hybridization library from potato skin was performed. This library yielded a comprehensive list of 108 candidate genes that were manually sorted in functional categories according to the main cellular and metabolic processes in periderm. As expected, the list contains Suberin and wax genes, including some genes with a demonstrated role in the biosynthesis of these cell wall aliphatic compounds. Moreover, Regulation and Stress and defence genes are highly abundant in the library in general agreement with previous potato skin proteomic studies. The putative function of the genes in periderm is discussed.

  11. Construction of human antibody gene libraries and selection of antibodies by phage display.

    PubMed

    Frenzel, André; Kügler, Jonas; Wilke, Sonja; Schirrmann, Thomas; Hust, Michael

    2014-01-01

    Antibody phage display is the most commonly used in vitro selection technology and has yielded thousands of useful antibodies for research, diagnostics, and therapy.The prerequisite for successful generation and development of human recombinant antibodies using phage display is the construction of a high-quality antibody gene library. Here, we describe the methods for the construction of human immune and naive scFv gene libraries.The success also depends on the panning strategy for the selection of binders from these libraries. In this article, we describe a panning strategy that is high-throughput compatible and allows parallel selection in microtiter plates.

  12. K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries

    PubMed Central

    Jangid, Kamlesh; Kao, Ming-Hung; Lahamge, Aishwarya; Williams, Mark A.; Rathbun, Stephen L.; Whitman, William B.

    2016-01-01

    K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley’s K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing. PMID:27911946

  13. K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries.

    PubMed

    Jangid, Kamlesh; Kao, Ming-Hung; Lahamge, Aishwarya; Williams, Mark A; Rathbun, Stephen L; Whitman, William B

    2016-01-01

    K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley's K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing.

  14. Automating gene library synthesis by structure-based combinatorial protein engineering: examples from plant sesquiterpene synthases.

    PubMed

    Dokarry, Melissa; Laurendon, Caroline; O'Maille, Paul E

    2012-01-01

    Structure-based combinatorial protein engineering (SCOPE) is a homology-independent recombination method to create multiple crossover gene libraries by assembling defined combinations of structural elements ranging from single mutations to domains of protein structure. SCOPE was originally inspired by DNA shuffling, which mimics recombination during meiosis, where mutations from parental genes are "shuffled" to create novel combinations in the resulting progeny. DNA shuffling utilizes sequence identity between parental genes to mediate template-switching events (the annealing and extension of one parental gene fragment on another) in PCR reassembly reactions to generate crossovers and hence recombination between parental genes. In light of the conservation of protein structure and degeneracy of sequence, SCOPE was developed to enable the "shuffling" of distantly related genes with no requirement for sequence identity. The central principle involves the use of oligonucleotides to encode for crossover regions to choreograph template-switching events during PCR assembly of gene fragments to create chimeric genes. This approach was initially developed to create libraries of hybrid DNA polymerases from distantly related parents, and later developed to create a combinatorial mutant library of sesquiterpene synthases to explore the catalytic landscapes underlying the functional divergence of related enzymes. This chapter presents a simplified protocol of SCOPE that can be integrated with different mutagenesis techniques and is suitable for automation by liquid-handling robots. Two examples are presented to illustrate the application of SCOPE to create gene libraries using plant sesquiterpene synthases as the model system. In the first example, we outline how to create an active-site library as a series of complex mixtures of diverse mutants. In the second example, we outline how to create a focused library as an array of individual clones to distil minimal combinations of

  15. Extensive libraries of gene truncation variants generated by in vitro transposition.

    PubMed

    Morelli, Aleardo; Cabezas, Yari; Mills, Lauren J; Seelig, Burckhard

    2017-01-26

    The detailed analysis of the impact of deletions on proteins or nucleic acids can reveal important functional regions and lead to variants with improved macromolecular properties. We present a method to generate large libraries of mutants with deletions of varying length that are randomly distributed throughout a given gene. This technique facilitates the identification of crucial sequence regions in nucleic acids or proteins. The approach utilizes in vitro transposition to generate 5' and 3' fragment sub-libraries of a given gene, which are then randomly recombined to yield a final library comprising both terminal and internal deletions. The method is easy to implement and can generate libraries in three to four days. We used this approach to produce a library of >9000 random deletion mutants of an artificial RNA ligase enzyme representing 32% of all possible deletions. The quality of the library was assessed by next-generation sequencing and detailed bioinformatics analysis. Finally, we subjected this library to in vitro selection and obtained fully functional variants with deletions of up to 18 amino acids of the parental enzyme that had been 95 amino acids in length.

  16. PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries.

    PubMed

    Potvin, Marianne; Lovejoy, Connie

    2009-01-01

    Environmental clone libraries constructed using small subunit ribosomal RNA (rRNA) or other gene-specific primers have become the standard molecular approach for identifying microorganisms directly from their environment. This technique includes an initial polymerase chain reaction (PCR) amplification step of a phylogenetically useful marker gene using universal primers. Although it is acknowledged that such primers introduce biases, there have been few studies if any to date systematically examining such bias in eukaryotic microbes. We investigated some implications of such bias by constructing clone libraries using several universal primer pairs targeting rRNA genes. Firstly, we constructed artificial libraries using a known mix of small cultured pelagic arctic algae with representatives from five major lineages and secondly we investigated environmental samples using several primer pairs. No primer pair retrieved all of the original algae in the artificial clone libraries and all showed a favorable bias toward the dinoflagellate Polarella glacialis and a bias against the prasinophyte Micromonas and a pennate diatom. Several other species were retrieved by only one primer pair tested. Despite this, sequences from nine environmental libraries were diverse and contained representatives from all major eukaryotic clades expected in marine samples. Further, libraries from the same sample grouped together using Bray-Curtis clustering, irrespective of primer pairs. We conclude that environmental PCR-based techniques are sufficient to compare samples, but the total diversity will probably always be underestimated and relative abundance estimates should be treated with caution.

  17. Construction of a gene library from Azospirillum brasilense and characterization of a recombinant containing the nif structural genes.

    PubMed

    Schrank, I S; Zaha, A; de Araújo, E F; Santos, D S

    1987-01-01

    1. We have constructed a gene library, from Azospirillum brasilense using the vector EMBL4. 2. A recombinant containing the nif structural genes from A. brasilense was isolated and characterized. This recombinant contains a DNA insert of about 15 kilobases (kb) which gives rise to five fragments after cleavage with EcoRI. Only one of the DNA fragments (6.5 kb) hybridized to the nifHDK genes of Klebsiella pneumoniae. 3. The organization of the nif genes in this DNA fragment was determined using different DNA segments containing the nifH, nifK or nifD genes of K. pneumoniae as probes.

  18. Genes expressed in cotton (Gossypium hirsutum) buds isolated with a subtractive library.

    PubMed

    Pinheiro, M P N; Batista, V G L; Martins, N F; Santos, R C; Melo Filho, P A; Silva, C R C; Lima, L M

    2013-01-16

    A subtractive cDNA library from cotton buds was constructed to prospect for differentially expressed genes related to early bud development. A library was constructed and 768 cDNA sequences were obtained, comprising 168 clusters, with 126 contigs and 42 singlets. Both the Gossypium as well as Arabidopsis databases were utilized for the in silico analysis, since some genes identified in cotton have not yet been studied for functionality, although they have homology with genes from other species. The transcriptome revealed a large number of transcripts, some of them with unknown function, and others related to pollen development, pollen tubes, ovules, and fibers at different stages. The most populated contig was identified as fiber from 0-10 days after anthesis, with 12 reads. The success and novelty rates generated from the library were 67 and 51%, respectively. The information obtained here will provide a framework for research on functional cotton genomics.

  19. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules.

    PubMed

    Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried

    2015-01-01

    A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.

  20. 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.

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

    PubMed

    Rabinowicz, Pablo D

    2003-01-01

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

  2. A Census of rRNA Genes and Linked Genomic Sequences within a Soil Metagenomic Library

    PubMed Central

    Liles, Mark R.; Manske, Brian F.; Bintrim, Scott B.; Handelsman, Jo; Goodman, Robert M.

    2003-01-01

    We have analyzed the diversity of microbial genomes represented in a library of metagenomic DNA from soil. A total of 24,400 bacterial artificial chromosome (BAC) clones were screened for 16S rRNA genes. The sequences obtained from BAC clones were compared with a collection generated by direct PCR amplification and cloning of 16S rRNA genes from the same soil. The results indicated that the BAC library had substantially lower representation of bacteria among the Bacillus, α-Proteobacteria, and CFB groups; greater representation among the β- and γ-Proteobacteria, and OP10 divisions; and no rRNA genes from the domains Eukaryota and Archaea. In addition to rRNA genes recovered from the bacterial divisions Proteobacteria, Verrucomicrobia, Firmicutes, Cytophagales, and OP11, we identified many rRNA genes from the BAC library affiliated with the bacterial division Acidobacterium; all of these sequences were affiliated with subdivisions that lack cultured representatives. The complete sequence of one BAC clone derived from a member of the Acidobacterium division revealed a complete rRNA operon and 20 other open reading frames, including predicted gene products involved in cell division, cell cycling, folic acid biosynthesis, substrate metabolism, amino acid uptake, DNA repair, and transcriptional regulation. This study is the first step in using genomics to reveal the physiology of as-yet-uncultured members of the Acidobacterium division. PMID:12732537

  3. Restriction enzyme-free construction of random gene mutagenesis libraries in Escherichia coli.

    PubMed

    Pai, Jen C; Entzminger, Kevin C; Maynard, Jennifer A

    2012-02-15

    Directed evolution relies on both random and site-directed mutagenesis of individual genes and regulatory elements to create variants with altered activity profiles for engineering applications. Central to these experiments is the construction of large libraries of related variants. However, a number of technical hurdles continue to limit routine construction of random mutagenesis libraries in Escherichia coli, in particular, inefficiencies during digestion and ligation steps. Here, we report a restriction enzyme-free approach to library generation using megaprimers termed MegAnneal. Target DNA is first exponentially amplified using error-prone polymerase chain reaction (PCR) and then linearly amplified with a single 3' primer to generate long, randomly mutated, single-stranded megaprimers. These are annealed to single-stranded dUTP-containing template plasmid and extended with T7 polymerase to create a complementary strand, and the resulting termini are ligated with T4 DNA ligase. Using this approach, we are able to reliably generate libraries of approximately 10⁷ colony-forming units (cfu)/μg DNA/transformation in a single day. We have created MegAnneal libraries based on three different single-chain antibodies and identified variants with enhanced expression and ligand-binding affinity. The key advantages of this approach include facile amplification, restriction enzyme-free library generation, and a significantly reduced risk of mutations outside the targeted region and wild-type contamination as compared with current methods.

  4. Mining expressed sequence tag (EST) libraries for cancer-associated genes.

    PubMed

    Schmitt, Armin O

    2010-01-01

    Originally established in the beginning of the 1990s as a direct route to gene finding, expressed sequence tags (ESTs) still lend themselves as a means to analyze gene expression in almost all human tissues. The type of questions that can be addressed using public EST libraries ranges from tissue-specific gene profiling to the comparison between tissues in diseased and healthy states. Thanks to a multitude of web-based online bioinformatics resources, mining in EST libraries is not restricted to experts in the field of data analysis, but can readily be performed by the medical or life scientist. In this chapter, a couple of cases studies are presented that guide the scientist to the most useful online resources so that they can conduct their own research.

  5. An episomal expression vector for screening mutant gene libraries in Pichia pastoris.

    PubMed

    Lee, Charles C; Williams, Tina G; Wong, Dominic W S; Robertson, George H

    2005-07-01

    Screening mutant gene libraries for isolating improved enzyme variants is a powerful technique that benefits from effective and reliable biological expression systems. Pichia pastoris is a very useful organism to express proteins that are inactive in other hosts such as Escherichia coli and Saccharomyces cerevisiae. However, most P. pastoris expression plasmids are designed to integrate into the host chromosome and hence are not as amenable to high-throughput screening projects. We have designed a P. pastoris expression vector, pBGP1, incorporating an autonomous replication sequence that allows the plasmid to exist as an episomal element. This vector contains the alpha-factor signal sequence to direct secretion of the mutant enzymes. Expression of the genes is driven by the constitutive GAP promoter, thus eliminating the need for timed or cell density-specific inductions. The pBGP1 plasmid was used to screen a xylanase gene library to isolate higher activity mutants.

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

    PubMed Central

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

    1982-01-01

    Using a cDNA clone for the histone H3 we have isolated, from two genomic libraries of Xenopus laevis and Xenopus tropicalis, clones containing four different histone gene clusters. The structural organization of X. laevis histone genes has been determined by restriction mapping, Southern blot hybridization and translation of the mRNAs which hybridize to the various restriction fragments. The arrangement of the histone genes in X. tropicalis has been determined by Southern analysis using X. laevis genomic fragments, containing individual genes, as probes. Histone genes are clustered in the genome of X. laevis and X. tropicalis and, compared to invertebrates, show a higher organization heterogeneity as demonstrated by structural analysis of the four genomic clones. In fact, the order of the genes within individual clusters is not conserved. Images PMID:6296782

  7. Identification of pathogenetically relevant genes in lymphomagenesis by shRNA library screens.

    PubMed

    Ngo, Vu N

    2013-01-01

    RNA interference (RNAi) is a conserved posttranscriptional gene silencing mechanism that has recently emerged as a breakthrough genetic tool in functional genomics and drug target discovery. An increasing number of studies applying RNAi in high-throughput screens have begun to unravel complex signaling networks underlying diverse cellular processes. This chapter describes an approach to construct a conditional small-hairpin (sh)RNA library and its application in human lymphoma cell lines. A library cloning procedure outlines the incorporation of shRNA sequences and random 60-mer "bar code" oligonucleotides, enabling rapid identification of the hairpin by microarrays. Lymphoma cell lines are optimized for efficient retroviral transduction and tetracycline inducibility. The shRNA library is suitable for identifying molecular targets in cancer, but also versatile for various screening strategies.

  8. The evolution of secondary organization in immune system gene libraries

    SciTech Connect

    Hightower, R.; Forrest, S.; Perelson, A.S.

    1993-02-01

    A binary model of the immune system is used to study the effects of evolution on the genetic encoding for antibody molecules. We report experiments which show that the evolution of immune system genes, simulated by the genetic algorithm, can induce a high degree of genetic organization even though that organization is not explicitly required by the fitness function. This secondary organization is related to the true fitness of an individual, in contrast to the sampled fitness which is the explicit fitness measure used to drive the process of evolution.

  9. Construction of differentially expressed genes library of bighead carp (Aristichthys nobilis) exposed to microcystin-lr using ssh and expression profile of related genes.

    PubMed

    Cui, Zhihui; Zhang, Kaiyue; Qu, Xiancheng; Liu, Qigen

    2011-12-01

    Microcystins (MCs) are hepatotoxic cyclic heptapeptides produced by cyanobacteria (blue-green algae). There are more than 70 MCs variants of which the most common and widely studied is MC-LR. We screened the hepatocellular differentially expressed genes against MC-LR in the bighead carp (Aristichthys nobilis). Suppression subtractive hybridization was used to construct the forward subtracted and reverse subtracted cDNA libraries, and one hundred and thirty two positive clones (seventy one in forward library and sixty one in reverse library) were randomly selected and sequenced. Finally, fifty five reliable sequences from the forward subtracted library were used in a homology search by BLASTn and BLASTx, as were 57 reliable sequences from the reverse subtracted library. Furthermore, eight analyzed sequences from the forward subtracted cDNA library and seven from the reverse subtracted library were found to be non-homologous sequences. The screening identified genes induced by MC-LR in both libraries that are involved in various processes, such as energy metabolism, immunity, and apoptosis. Some are cytoskeleton- and transportation-related genes, while signal transduction-related genes were also found. Significant genes, such as the apoptosis-related gene p53 and the proto-oncogene c-myc, are involved in inhibition of the MC-LR response in the reverse subtracted library. In addition, several immune-related genes, which play an important role in antioxidation and detoxification of MC-LR, were characterized and identified in both of the subtracted libraries. The study provides the basic data to further identify the genes and molecular mechanism of detoxification of microcystins.

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

    PubMed Central

    2011-01-01

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

  11. Sequence analysis of a rainbow trout cDNA library and creation of a gene index.

    PubMed

    Rexroad, C E; Lee, Y; Keele, J W; Karamycheva, S; Brown, G; Koop, B; Gahr, S A; Palti, Y; Quackenbush, J

    2003-01-01

    Expressed sequence tag (EST) projects have produced extremely valuable resources for identifying genes affecting phenotypes of interest. A large-scale EST sequencing project for rainbow trout was initiated to identify and functionally annotate as many unique transcripts as possible. Over 45,000 5' ESTs were obtained by sequencing clones from a single normalized library constructed using mRNA from six tissues. The production of this sequence data and creation of a rainbow trout Gene Index eliminating redundancy and providing annotation for these sequences will facilitate research in this species.

  12. 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.

  13. Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

    PubMed

    Dai, Zhimin; Guo, Xue; Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

    2014-01-01

    Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.

  14. Identification of Nitrogen-Fixing Genes and Gene Clusters from Metagenomic Library of Acid Mine Drainage

    PubMed Central

    Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

    2014-01-01

    Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community. PMID:24498417

  15. Function-Based Metagenomic Library Screening and Heterologous Expression Strategy for Genes Encoding Phosphatase Activity.

    PubMed

    Villamizar, Genis A Castillo; Nacke, Heiko; Daniel, Rolf

    2017-01-01

    The release of phosphate from inorganic and organic phosphorus compounds can be mediated enzymatically. Phosphate-releasing enzymes, comprising acid and alkaline phosphatases, are recognized as useful biocatalysts in applications such as plant and animal nutrition, bioremediation and diagnostic analysis. Metagenomic approaches provide access to novel phosphatase-encoding genes. Here, we describe a function-based screening approach for rapid identification of genes conferring phosphatase activity from small-insert and large-insert metagenomic libraries derived from various environments. This approach bears the potential for discovery of entirely novel phosphatase families or subfamilies and members of known enzyme classes hydrolyzing phosphomonoester bonds such as phytases. In addition, we provide a strategy for efficient heterologous phosphatase gene expression.

  16. New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras†

    PubMed Central

    Ashelford, Kevin E.; Chuzhanova, Nadia A.; Fry, John C.; Jones, Antonia J.; Weightman, Andrew J.

    2006-01-01

    A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts. Written in the Java computer language and capable of running on all major operating systems, the program provides a novel graphical approach for visualizing phylogenetic relationships among 16S rRNA gene sequences. To illustrate its use, we analyzed most of the large libraries of cloned bacterial 16S rRNA gene sequences submitted to the public repository during 2005. Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission. Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/. PMID:16957188

  17. Genomic Library Screens for Genes Involved in n-Butanol Tolerance in Escherichia coli

    PubMed Central

    Reyes, Luis H.; Almario, Maria P.; Kao, Katy C.

    2011-01-01

    Background n-Butanol is a promising emerging biofuel, and recent metabolic engineering efforts have demonstrated the use of several microbial hosts for its production. However, most organisms have very low tolerance to n-butanol (up to 2% (v/v)), limiting the economic viability of this biofuel. The rational engineering of more robust n-butanol production hosts relies upon understanding the mechanisms involved in tolerance. However, the existing knowledge of genes involved in n-butanol tolerance is limited. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance. Methodology/Principal Findings Using a genomic library enrichment strategy, we identified approximately 270 genes that were enriched or depleted in n-butanol challenge. The effects of these candidate genes on n-butanol tolerance were experimentally determined using overexpression or deletion libraries. Among the 55 enriched genes tested, 11 were experimentally shown to confer enhanced tolerance to n-butanol when overexpressed compared to the wild-type. Among the 84 depleted genes tested, three conferred increased n-butanol resistance when deleted. The overexpressed genes that conferred the largest increase in n-butanol tolerance were related to iron transport and metabolism, entC and feoA, which increased the n-butanol tolerance by 32.8±4.0% and 49.1±3.3%, respectively. The deleted gene that resulted in the largest increase in resistance to n-butanol was astE, which enhanced n-butanol tolerance by 48.7±6.3%. Conclusions/Significance We identified and experimentally verified 14 genes that decreased the inhibitory effect of n-butanol tolerance on E. coli. From the data, we were able to expand the current knowledge on the genes involved in n-butanol tolerance; the results suggest that an increased iron transport and metabolism and decreased acid resistance may enhance n-butanol tolerance. The genes and mechanisms identified in this study will be helpful in the

  18. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

    PubMed Central

    Horlbeck, Max A; Gilbert, Luke A; Villalta, Jacqueline E; Adamson, Britt; Pak, Ryan A; Chen, Yuwen; Fields, Alexander P; Park, Chong Yon; Corn, Jacob E; Kampmann, Martin; Weissman, Jonathan S

    2016-01-01

    We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accurately predict highly effective single guide RNAs (sgRNAs) for targeting nuclease-dead Cas9-mediated transcriptional repression (CRISPRi) and activation (CRISPRa). We use this algorithm to design next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. A CRISPRi screen for essential genes in K562 cells demonstrates that the large majority of sgRNAs are highly active. We also find CRISPRi does not exhibit any detectable non-specific toxicity recently observed with CRISPR nuclease approaches. Precision-recall analysis shows that we detect over 90% of essential genes with minimal false positives using a compact 5 sgRNA/gene library. Our results establish CRISPRi and CRISPRa as premier tools for loss- or gain-of-function studies and provide a general strategy for identifying Cas9 target sites. DOI: http://dx.doi.org/10.7554/eLife.19760.001 PMID:27661255

  19. In-depth cDNA library sequencing provides quantitative gene expression profiling in cancer biomarker discovery.

    PubMed

    Yang, Wanling; Ying, Dingge; Lau, Yu-Lung

    2009-06-01

    Quantitative gene expression analysis plays an important role in identifying differentially expressed genes in various pathological states, gene expression regulation and co-regulation, shedding light on gene functions. Although microarray is widely used as a powerful tool in this regard, it is suboptimal quantitatively and unable to detect unknown gene variants. Here we demonstrated effective detection of differential expression and co-regulation of certain genes by expressed sequence tag analysis using a selected subset of cDNA libraries. We discussed the issues of sequencing depth and library preparation, and propose that increased sequencing depth and improved preparation procedures may allow detection of many expression features for less abundant gene variants. With the reduction of sequencing cost and the emerging of new generation sequencing technology, in-depth sequencing of cDNA pools or libraries may represent a better and powerful tool in gene expression profiling and cancer biomarker detection. We also propose using sequence-specific subtraction to remove hundreds of the most abundant housekeeping genes to increase sequencing depth without affecting relative expression ratio of other genes, as transcripts from as few as 300 most abundantly expressed genes constitute about 20% of the total transcriptome. In-depth sequencing also represents a unique advantage of detecting unknown forms of transcripts, such as alternative splicing variants, fusion genes, and regulatory RNAs, as well as detecting mutations and polymorphisms that may play important roles in disease pathogenesis.

  20. Analysis of SSH library of rice variety Aganni reveals candidate gall midge resistance genes.

    PubMed

    Divya, Dhanasekar; Singh, Y Tunginba; Nair, Suresh; Bentur, J S

    2016-03-01

    The Asian rice gall midge, Orseolia oryzae, is a serious insect pest causing extensive yield loss. Interaction between the gall midge and rice genotypes is known to be on a gene-for-gene basis. Here, we report molecular basis of HR- (hypersensitive reaction-negative) type of resistance in Aganni (an indica rice variety possessing gall midge resistance gene Gm8) through the construction and analysis of a suppressive subtraction hybridization (SSH) cDNA library. In all, 2,800 positive clones were sequenced and analyzed. The high-quality ESTs were assembled into 448 non-redundant gene sequences. Homology search with the NCBI databases, using BlastX and BlastN, revealed that 73% of the clones showed homology to genes with known function and majority of ESTs belonged to the gene ontology category 'biological process'. Validation of 27 putative candidate gall midge resistance genes through real-time PCR, following gall midge infestation, in contrasting parents and their derived pre-NILs (near isogenic lines) revealed induction of specific genes related to defense and metabolism. Interestingly, four genes, belonging to families of leucine-rich repeat (LRR), heat shock protein (HSP), pathogenesis related protein (PR), and NAC domain-containing protein, implicated in conferring HR+ type of resistance, were found to be up-regulated in Aganni. Two of the reactive oxygen intermediates (ROI)-scavenging-enzyme-coding genes Cytosolic Ascorbate Peroxidase1, 2 (OsAPx1 and OsAPx2) were found up-regulated in Aganni in incompatible interaction possibly suppressing HR. We suggest that Aganni has a deviant form of inducible, salicylic acid (SA)-mediated resistance but without HR.

  1. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.

    PubMed

    Jacquiod, Samuel; Demanèche, Sandrine; Franqueville, Laure; Ausec, Luka; Xu, Zhuofei; Delmont, Tom O; Dunon, Vincent; Cagnon, Christine; Mandic-Mulec, Ines; Vogel, Timothy M; Simonet, Pascal

    2014-11-20

    A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.

  2. Identification of genes that function in the TNF-alpha-mediated apoptotic pathway using randomized hybrid ribozyme libraries.

    PubMed

    Kawasaki, Hiroaki; Onuki, Reiko; Suyama, Eigo; Taira, Kazunari

    2002-04-01

    Now that the sequences of many genomes are available, methods are required for the rapid identification of functional genes. We describe here a simple system for the isolation of genes that function in the tumor necrosis factor-alpha (TNF-alpha)-mediated pathway of apoptosis, using RNA helicase-associated ribozyme libraries with randomized substrate-binding arms. Because target-site accessibility considerably limits the effective use of intracellular ribozymes, the effectiveness of a conventional ribozyme library has been low. To overcome this obstacle, we attached to ribozymes an RNA motif (poly(A)-tail) able to interact with endogenous RNA helicase(s) so that the resulting helicase-attached, hybrid ribozymes can more easily attack target sites regardless of their secondary or tertiary structures. When the phenotype of cells changes upon introduction of a ribozyme library, genes responsible for these changes may be identified by sequencing the active ribozyme clones. In the case of TNF-alpha-mediated apoptosis, when a ribozyme library was introduced into MCF-7 cells, surviving clones were completely or partially resistant to TNF-alpha-induced apoptosis. We identified many pro-apoptotic genes and partial sequences of previously uncharacterized genes using this method. Our gene discovery system should be generally applicable to the identification of functional genes in various systems.

  3. 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.

  4. Isolation and characterization of rice cesium transporter genes from a rice-transporter-enriched yeast expression library.

    PubMed

    Yamaki, Tomohiro; Otani, Masahiro; Ono, Kohei; Mimura, Takuro; Oda, Koshiro; Minamii, Takeshi; Matsumoto, Shingo; Matsuo, Yuzy; Kawamukai, Makoto; Akihiro, Takashi

    2017-03-28

    A considerable portion of agricultural land in central-east Japan has been contaminated by radioactive material, particularly radioactive Cs, due to the industrial accident at the Fukushima Daiichi nuclear power plant. Understanding the mechanism of absorption, translocation, and accumulation of Cs(+) in plants will greatly assist in developing approaches to help reduce the radioactive contamination of agricultural products. At present, however, little is known regarding the Cs(+) transporters in rice. A transporter-enriched yeast expression library was constructed and the library was screened for Cs(+) transporter genes. The 1452 full length cDNAs encoding transporter genes were obtained from the Rice Genome Resource Center and 1358 clones of these transporter genes were successively subcloned into yeast expression vectors; which were then transferred into yeast. Using this library, both positive and negative selection screens can be performed, which have not been previously possible. The constructed library is an excellent tool for the isolation of novel transporter genes. This library was screened for clones that were sensitive to Cs(+) using a SD-Gal medium containing either 30 or 70 mM CsCl; resulting in the isolation of thirteen Cs(+) sensitive clones. (137) Cs absorption experiments were conducted and confirmed that all of the identified clones were able to absorb (137) Cs. Three potassium transporters, two ABC transporters, and one NRAMP transporter were among the thirteen identified clones.

  5. Construction and characterization of two Citrus BAC libraries and identification of clones containing the phytoene synthase gene.

    PubMed

    Baig, M N R; Yu, An; Guo, Wenwu; Deng, Xiuxin

    2009-05-01

    Two deep-coverage Bacterial Artificial Chromosome (BAC) libraries of Citrus sinensis (L.) Osbeck 'Cara Cara' navel orange and Citrus reticulata (L.) Blanco 'Egan No. 1' Ponkan mandarin, which belong to the two most important species of the Citrus genus, have been constructed and characterized to facilitate gene cloning and to analyze variety-specific genome composition. The C. sinensis BAC library consists of 36 000 clones with negligible false-positive clones and an estimated average insert size of 126 kb covering ~4.5 x 109 bp and thus providing an 11.8-fold coverage of haploid genome equivalents, whereas the C. reticulata library consists of 21 000 clones also with negligible false-positive clones and an estimated average of 120 kb covering ~2.5 x 109 bp representing a 6.6-fold coverage of haploid genome equivalents. Both libraries were evaluated for contamination with high-copy vector, empty pIndigoBAC536 vector, and organellar DNA sequences. Screening has been performed by Southern hybridization of BAC filters, which results in <0.5% chloroplast DNA contamination and no mitochondrial DNA contamination in both libraries. Eight and five positive clones harboring the gene encoding Phytoene synthase (Psy (EC 2.5.1.32)) were identified from the C. sinensis and C. reticulata libraries, respectively, using the filter hybridization procedure. These results suggest that the two BAC libraries are useful tools for the isolation of functional genes and advanced genomics research in the two important species C. sinensis and C. reticulata. Resources, high-density filters, individual clones, and whole libraries are available for public distribution and are accessible at the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University.

  6. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen suppressive soil

    SciTech Connect

    Hjort, K.; Bergstrom, M.; Adesina, M.F.; Jansson, J.K.; Smalla, K.; Sjoling, S.

    2009-09-01

    Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal-restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal-restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF{sup 103} of the isolate, Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

  7. From the Cover: A polymer library approach to suicide gene therapy for cancer

    NASA Astrophysics Data System (ADS)

    Anderson, Daniel G.; Peng, Weidan; Akinc, Akin; Hossain, Naushad; Kohn, Anat; Padera, Robert; Langer, Robert; Sawicki, Janet A.

    2004-11-01

    Optimal gene therapy for cancer must (i) deliver DNA to tumor cells with high efficiency, (ii) induce minimal toxicity, and (iii) avoid gene expression in healthy tissues. To this end, we generated a library of >500 degradable, poly(-amino esters) for potential use as nonviral DNA vectors. Using high-throughput methods, we screened this library in vitro for transfection efficiency and cytotoxicity. We tested the best performing polymer, C32, in mice for toxicity and DNA delivery after intratumor and i.m. injection. C32 delivered DNA intratumorally 4-fold better than one of the best commercially available reagents, jetPEI (polyethyleneimine), and 26-fold better than naked DNA. Conversely, the highest transfection levels after i.m. administration were achieved with naked DNA, followed by polyethyleneimine; transfection was rarely observed with C32. Additionally, polyethyleneimine induced significant local toxicity after i.m. injection, whereas C32 demonstrated no toxicity. Finally, we used C32 to deliver a DNA construct encoding the A chain of diphtheria toxin (DT-A) to xenografts derived from LNCaP human prostate cancer cells. This construct regulates toxin expression both at the transcriptional level by the use of a chimeric-modified enhancer/promoter sequence of the human prostate-specific antigen gene and by DNA recombination mediated by Flp recombinase. C32 delivery of the A chain of diphtheria toxin DNA to LNCaP xenografts suppressed tumor growth and even caused 40% of tumors to regress in size. Because C32 transfects tumors locally at high levels, transfects healthy muscle poorly, and displays no toxicity, it may provide a vehicle for the local treatment of cancer. prostate | cationic polymers

  8. Identification and characterization of a cellulase-encoding gene from the buffalo rumen metagenomic library.

    PubMed

    Nguyen, Nhung Hong; Maruset, Lalita; Uengwetwanit, Tanaporn; Mhuantong, Wuttichai; Harnpicharnchai, Piyanun; Champreda, Verawat; Tanapongpipat, Sutipa; Jirajaroenrat, Kanya; Rakshit, Sudip K; Eurwilaichitr, Lily; Pongpattanakitshote, Somchai

    2012-01-01

    Microorganisms residing in the rumens of cattle represent a rich source of lignocellulose-degrading enzymes, since their diet consists of plant-based materials that are high in cellulose and hemicellulose. In this study, a metagenomic library was constructed from buffalo rumen contents using pCC1FOS fosmid vector. Ninety-three clones from the pooled library of approximately 10,000 clones showed degrading activity against AZCL-HE-Cellulose, whereas four other clones showed activity against AZCL-Xylan. Contig analysis of pyrosequencing data derived from the selected strongly positive clones revealed 15 ORFs that were closely related to lignocellulose-degrading enzymes belonging to several glycosyl hydrolase families. Glycosyl hydrolase family 5 (GHF5) was the most abundant glycosyl hydrolase found, and a majority of the GHF5s in our metagenomes were closely related to several ruminal bacteria, especially ones from other buffalo rumen metagenomes. Characterization of BT-01, a selected clone with highest cellulase activity from the primary plate screening assay, revealed a cellulase encoding gene with optimal working conditions at pH 5.5 at 50 °C. Along with its stability over acidic pH, the capability efficiently to hydrolyze cellulose in feed for broiler chickens, as exhibited in an in vitro digestibility test, suggests that BT-01 has potential application as a feed supplement.

  9. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

    SciTech Connect

    Gihring, Thomas; Green, Stefan; Schadt, Christopher Warren

    2011-01-01

    Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g. Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.

  10. Changes in the Composition of Drinking Water Bacterial Clone Libraries Introduced by Using Two Different 16S rRna Gene PCR Primers

    EPA Science Inventory

    Sequence analysis of 16S rRNA gene clone libraries is a popular tool used to describe the composition of natural microbial communities. Commonly, clone libraries are developed by direct cloning of 16S rRNA gene PCR products. Different primers are often employed in the initial amp...

  11. Changes in the Composition of Drinking Water Bacterial Clone Libraries Introduced by Using Two Different 16S rRNA Gene PCR Primers

    EPA Science Inventory

    Sequence analysis of 16S rRNA gene clone libraries is a popular tool used to describe the composition of natural microbial communities. Commonly, clone libraries are developed by direct cloning of 16S rRNA gene PCR products. Different primers are often employed in the initial amp...

  12. Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

    PubMed Central

    Silva, Cynthia C.; Hayden, Helen; Sawbridge, Tim; Mele, Pauline; De Paula, Sérgio O.; Silva, Lívia C. F.; Vidigal, Pedro M. P.; Vicentini, Renato; Sousa, Maíra P.; Torres, Ana Paula R.; Santiago, Vânia M. J.; Oliveira, Valéria M.

    2013-01-01

    Two fosmid libraries, totaling 13,200 clones, were obtained from bioreactor sludge of petroleum refinery wastewater treatment system. The library screening based on PCR and biological activity assays revealed more than 400 positive clones for phenol degradation. From these, 100 clones were randomly selected for pyrosequencing in order to evaluate the genetic potential of the microorganisms present in wastewater treatment plant for biodegradation, focusing mainly on novel genes and pathways of phenol and aromatic compound degradation. The sequence analysis of selected clones yielded 129,635 reads at an estimated 17-fold coverage. The phylogenetic analysis showed Burkholderiales and Rhodocyclales as the most abundant orders among the selected fosmid clones. The MG-RAST analysis revealed a broad metabolic profile with important functions for wastewater treatment, including metabolism of aromatic compounds, nitrogen, sulphur and phosphorus. The predicted 2,276 proteins included phenol hydroxylases and cathecol 2,3- dioxygenases, involved in the catabolism of aromatic compounds, such as phenol, byphenol, benzoate and phenylpropanoid. The sequencing of one fosmid insert of 33 kb unraveled the gene that permitted the host, Escherichia coli EPI300, to grow in the presence of aromatic compounds. Additionally, the comparison of the whole fosmid sequence against bacterial genomes deposited in GenBank showed that about 90% of sequence showed no identity to known sequences of Proteobacteria deposited in the NCBI database. This study surveyed the functional potential of fosmid clones for aromatic compound degradation and contributed to our knowledge of the biodegradative capacity and pathways of microbial assemblages present in refinery wastewater treatment system. PMID:23637911

  13. Systematic mining of salt-tolerant genes in halophyte-Zoysia matrella through cDNA expression library screening.

    PubMed

    Chen, Yu; Zong, Junqin; Tan, Zhiqun; Li, Lanlan; Hu, Baoyun; Chen, Chuanming; Chen, Jingbo; Liu, Jianxiu

    2015-04-01

    Though a large number of salt-tolerant genes were identified from Glycophyte in previous study, genes involved in salt-tolerance of halophyte were scarcely studied. In this report, an important halophyte turfgrass, Zoysia matrella, was used for systematic excavation of salt-tolerant genes using full-length cDNA expression library in yeast. Adopting the Gateway-compatible vector system, a high quality entry library was constructed, containing 3 × 10(6) clones with an average inserted fragments length of 1.64 kb representing a 100% full-length rate. The yeast expression library was screened in a salt-sensitive yeast mutant. The screening yielded dozens of salt-tolerant clones harboring 16 candidate salt-tolerant genes. Under salt-stress condition, these 16 genes exhibited different transcription levels. According to the results, we concluded that the salt-tolerance of Z. matrella might result from known genes involved in ion regulation, osmotic adjustment, as well as unknown pathway associated with protein folding and modification, RNA metabolism, and mitochondrial membrane translocase, etc. In addition, these results shall provide new insight for the future researches with respect to salt-tolerance.

  14. Characterization of Leukemia-Inducing Genes Using a Proto-Oncogene/Homeobox Gene Retroviral Human cDNA Library in a Mouse In Vivo Model.

    PubMed

    Jang, Su Hwa; Lee, Sohyun; Chung, Hee Yong

    2015-01-01

    The purpose of this research is to develop a method to screen a large number of potential driver mutations of acute myeloid leukemia (AML) using a retroviral cDNA library and murine bone marrow transduction-transplantation system. As a proof-of-concept, murine bone marrow (BM) cells were transduced with a retroviral cDNA library encoding well-characterized oncogenes and homeobox genes, and the virus-transduced cells were transplanted into lethally irradiated mice. The proto-oncogenes responsible for leukemia initiation were identified by PCR amplification of cDNA inserts from genomic DNA isolated from leukemic cells. In an initial screen of ten leukemic mice, the MYC proto-oncogene was detected in all the leukemic mice. Of ten leukemic mice, 3 (30%) had MYC as the only transgene, and seven mice (70%) had additional proto-oncogene inserts. We repeated the same experiment after removing MYC-related genes from the library to characterize additional leukemia-inducing gene combinations. Our second screen using the MYC-deleted proto-oncogene library confirmed MEIS1and the HOX family as cooperating oncogenes in leukemia pathogenesis. The model system we introduced in this study will be valuable in functionally screening novel combinations of genes for leukemogenic potential in vivo, and the system will help in the discovery of new targets for leukemia therapy.

  15. 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

  16. Construction and analysis of a suppression subtractive hybridization library of regeneration-related genes in soybean.

    PubMed

    Sun, J; Li, J; Liu, M; Zhang, B B; Li, D M; Wang, M; Zhang, C; Li, W B; Su, A Y; Wu, X X

    2015-01-30

    The development of a genetic transformation system is needed to address the problem of the low efficiency associated with soybean regeneration. To contribute to the enhancement of the soybean regenerative capacity, we explored the developmental mechanisms of soybean regeneration at the molecular level using a suppression subtractive hybridization cDNA library constructed from cotyledonary nodes of soybean cultivar DN50. A total of 918 positive clones were identified and screened, with most inserted fragments ranging from 100 to 750 bp. Of these, 411 differentially expressed functional expressed sequence tags were identified and annotated based on their similarity to orthologs and paralogs detected in GenBank using the nucleotide and translated nucleotide Basic Local Alignment Search Tools. Functional analysis revealed that the associated genes were involved in signal transduction, synthesis, and metabolism of macromolecules, glucose and protein synthesis and metabolism, light and leaf morphogenesis, regulation of apoptosis, cell defense, cell wall differentiation, and a variety of hormone and cytokinin-mediated signaling pathways. The information uncovered in our study should serve as a foundation for the establishment of an efficient and stable genetic transformation system for soybean regeneration.

  17. Systematic Isolation and Characterization of Cadmium Tolerant Genes in Tobacco: A cDNA Library Construction and Screening Approach

    PubMed Central

    Zhang, Mei; Mo, Hui; Sun, Wen; Guo, Yan; Li, Jing

    2016-01-01

    Heavy metal pollution is a major limiting factor that severely affects plant growth worldwide, and the accumulation of heavy metal in the plant may be hazardous to human health. To identify the processes involved in cadmium detoxification, we constructed a cDNA library of tobacco roots acclimated to cadmium (Cd) stress. According to the results of functional screening cDNA library with a yeast Cd-sensitive mutant, ycf1Δ, we obtained a series of candidate genes that were involved in Cd response. Sequence analysis and yeast functional complementation of 24 positive cDNA clones revealed that, in addition to antioxidant genes, genes implicated in abiotic and biotic stress defenses, cellular metabolism, and signal transduction showed Cd detoxification effects in yeast. The real time RT-PCR analyses revealed that some Cd tolerance/ detoxification genes may be able to anticipate in other stresses such as biotic defense and water balance in tobacco. Taken together, our data suggest that plants’ acclimation to Cd stress is a highly complex process associated with broad gene functions. Moreover, our results provide insights into the Cd detoxification mechanisms along with the antioxidant system, defense gene induction, and calcium signal pathway. PMID:27579677

  18. 16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development

    EPA Science Inventory

    The bacterial composition of chlorinated drinking water was analyzed using 16S rRNA gene clone libraries derived from DNA extracts of 12 samples and compared to clone libraries previously generated using RNA extracts from the same samples. Phylogenetic analysis of 761 DNA-based ...

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

    PubMed

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

    2012-01-01

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

  20. Structural analysis of the eukaryotic initiation factor 4E gene controlling potyvirus resistance in pepper: exploitation of a BAC library.

    PubMed

    Ruffel, Sandrine; Caranta, Carole; Palloix, Alain; Lefebvre, Véronique; Caboche, Michel; Bendahmane, Abdelhafid

    2004-09-01

    The pvr2 locus in pepper codes for a eukaryotic translation initiation factor 4E (eIF4E) gene that confers resistance to viruses belonging to the potyvirus genus. In this work, we describe the isolation and characterisation of the genomic sequence carrying the pvr2 locus. A Bacterial Artificial Chromosome (BAC) library that consisted of 239,232 clones with an average insert size of 123 kilobases (kb) was constructed from a Capsicum annuum line with the pvr2(+) allele for susceptibility to potato virus Y (PVY) and tobacco etch virus (TEV). Based on a polymerase chain reaction (PCR) screen with single-copy markers, three to seven positive BAC clones per markers were identified, indicating that the BAC library is suitable for pepper genome analysis. To determine the genomic organization of the pepper eIF4E gene, the library was screened with primers designed from the cDNA sequence and four positive BAC clones carrying the pvr2 locus were identified. A 7-kb DNA fragment containing the complete eIF4E gene was sub-cloned from the positive BAC clones and analysed. The eIF4E gene is organised into five exons and four introns and showed a strictly conserved exon/intron structure with eIF4E genes from Arabidopsis thaliana and rice. Moreover, the splice sites between plant exons 1/2 and 2/3 are conserved among eukaryotes including human, Drosophila and yeast. Several potential binding sites for MADS box transcription factors within the 5' flanking region of eIF4E genes from the three plant species were also predicted.

  1. Flow Cytometry-assisted Cloning of Specific Sequence Motifs fromComplex 16S ribosomal RNA Gene Libraries.

    SciTech Connect

    Nielsen, J.L.; Schramm, A.; Bernhard, A.E.; van den Engh, G.J.; Stahl, D.A.

    2004-07-21

    A flow cytometry method was developed for rapid screeningand recovery of cloned DNA containing common sequence motifs. Thisapproach, termed fluorescence-activated cell sorting-assisted cloning,was used to recover sequences affiliated with a unique lineage within theBacteroidetes not abundant in a clone library of environmental 16S rRNAgenes. Retrieval and sequence analysis of phylogenetically informativegenes has become a standard cultivation-independent technique toinvestigate microbial diversity in nature (7, 18). Genes encoding the 16SrRNA, because of the relative ease of their selective amplification, havebeen most frequently employed for general diversity surveys (16).Environmental studies have also focused on specific subpopulationsaffiliated with a phylogenetic group or identified by genes encodingspecific metabolic functions (e.g., ammonia oxidation, sulfaterespiration, and nitrate reduction) (8,15,20). However, specificpopulations may be of low abundance (1,23), or the genes encodingspecific metabolic functions may be insufficiently conserved to providepriming sites for general PCR amplification. Three general approacheshave been used to obtain 16S rRNA sequence information from low-abundancepopulations: screening hundreds to thousands of clones in a general 16SrRNA gene library (21), flow cytometric sorting of a subpopulation ofenvironmentally derived cells labeled by fluorescent in situhybridization (FISH) (27), or selective PCR amplification using primersspecific for the subpopulation (2,23). While the first approach is simplytime-consuming and tedious, the second has been restricted to fairlylarge and strongly fluorescent cells from aquatic samples (5, 27). Thethird approach often generates fragments of only a few hundred bases dueto the limited number of specific priming sites. Partial sequenceinformation often degrades analysis, obscuring or distorting thephylogenetic placement of the new sequences (11, 20). A more robustcharacterization of environ

  2. Construction of a directed hammerhead ribozyme library: towards the identification of optimal target sites for antisense-mediated gene inhibition.

    PubMed Central

    Pierce, M L; Ruffner, D E

    1998-01-01

    Antisense-mediated gene inhibition uses short complementary DNA or RNA oligonucleotides to block expression of any mRNA of interest. A key parameter in the success or failure of an antisense therapy is the identification of a suitable target site on the chosen mRNA. Ultimately, the accessibility of the target to the antisense agent determines target suitability. Since accessibility is a function of many complex factors, it is currently beyond our ability to predict. Consequently, identification of the most effective target(s) requires examination of every site. Towards this goal, we describe a method to construct directed ribozyme libraries against any chosen mRNA. The library contains nearly equal amounts of ribozymes targeting every site on the chosen transcript and the library only contains ribozymes capable of binding to that transcript. Expression of the ribozyme library in cultured cells should allow identification of optimal target sites under natural conditions, subject to the complexities of a fully functional cell. Optimal target sites identified in this manner should be the most effective sites for therapeutic intervention. PMID:9801305

  3. Discovery of Inhibitors of Aberrant Gene Transcription from Libraries of DNA Binding Molecules: Inhibition of LEF-1 Mediated Gene Transcription and Oncogenic Transformation

    PubMed Central

    Stover, James S.; Shi, Jin; Jin, Wei; Vogt, Peter K.; Boger, Dale L.

    2009-01-01

    The screening of a >9000 compound library of synthetic DNA binding molecules for selective binding to the consensus sequence of the transcription factor LEF-1 followed by assessment of the candidate compounds in a series of assays that characterized functional activity (disruption of DNA–LEF-1 binding) at the intended target and site (inhibition of intracellular LEF-1 mediated gene transcription) resulting in a desired phenotypic cellular change (inhibit LEF-1 driven cell transformation) provided two lead compounds: lefmycin-1 and lefmycin-2. The sequence of screens defining the approach assures that activity in the final functional assay may be directly related to the inhibition of gene transcription and DNA binding properties of the identified molecules. Central to the implementation of this generalized approach to the discovery of DNA binding small molecule inhibitors of gene transcription was: (1) the use of a technically non-demanding fluorescent intercalator displacement (FID) assay for initial assessment of the DNA binding affinity and selectivity of a library of compounds for any sequence of interest, and (2) the technology used to prepare a sufficiently large library of DNA binding compounds. PMID:19216569

  4. Discovery of inhibitors of aberrant gene transcription from Libraries of DNA binding molecules: inhibition of LEF-1-mediated gene transcription and oncogenic transformation.

    PubMed

    Stover, James S; Shi, Jin; Jin, Wei; Vogt, Peter K; Boger, Dale L

    2009-03-11

    The screening of a >9000 compound library of synthetic DNA binding molecules for selective binding to the consensus sequence of the transcription factor LEF-1 followed by assessment of the candidate compounds in a series of assays that characterized functional activity (disruption of DNA-LEF-1 binding) at the intended target and site (inhibition of intracellular LEF-1-mediated gene transcription) resulting in a desired phenotypic cellular change (inhibit LEF-1-driven cell transformation) provided two lead compounds: lefmycin-1 and lefmycin-2. The sequence of screens defining the approach assures that activity in the final functional assay may be directly related to the inhibition of gene transcription and DNA binding properties of the identified molecules. Central to the implementation of this generalized approach to the discovery of DNA binding small molecule inhibitors of gene transcription was (1) the use of a technically nondemanding fluorescent intercalator displacement (FID) assay for initial assessment of the DNA binding affinity and selectivity of a library of compounds for any sequence of interest, and (2) the technology used to prepare a sufficiently large library of DNA binding compounds.

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

    PubMed Central

    Nelson, William; Luo, Meizhong; Ma, Jianxin; Estep, Matt; Estill, James; He, Ruifeng; Talag, Jayson; Sisneros, Nicholas; Kudrna, David; Kim, HyeRan; Ammiraju, Jetty SS; Collura, Kristi; Bharti, Arvind K; Messing, Joachim; Wing, Rod A; SanMiguel, Phillip; Bennetzen, Jeffrey L; Soderlund, Carol

    2008-01-01

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

  6. Defining essential genes and identifying virulence factors of Porphyromonas gingivalis by massively-parallel sequencing of transposon libraries (Tn-seq)

    PubMed Central

    Klein, Brian A.; Duncan, Margaret J.; Hu, Linden T.

    2016-01-01

    Summary Porphyromonas gingivalis is a keystone pathogen in the development and progression of periodontal disease. Obstacles to the development of saturated transposon libraries have previously limited transposon mutant-based screens as well as essential gene studies. We have developed a system for efficient transposon mutagenesis of P. gingivalis using a modified mariner transposon. Tn-seq is a technique that allows for quantitative assessment of individual mutants within a transposon mutant library by sequencing the transposon-genome junctions and then compiling mutant presence by mapping to a base genome. Using Tn-seq, it is possible to quickly define all the insertional mutants in a library and thus identify non-essential genes under the conditions in which the library was produced. Identification of fitness of individual mutants under specific conditions can be performed by exposing the library to selective pressures. PMID:25636611

  7. CONSTRUCTION OF SILKWORM MIDGUT cDNA LIBRARY FOR SCREEN AND SEQUENCE ANALYSIS OF PERITROPHIC MEMBRANE PROTEIN GENES.

    PubMed

    Zhou, Yi-Jun; Xue, Bin; Li, Yang-Yang; Li, Fan-Chi; Ni, Min; Shen, Wei-De; Gu, Zhi-Ya; Li, Bing; Shen, Wei-De; Gu, Zhi-Ya; Li, Bing

    2016-01-01

    Silkworm is an important economic insect and the model species for Lepidoptera. The midgut of silkworm is an important physiological barrier, as its peritrophic membrane (PM) can resist pathogen invasion. In this study, a silkworm midgut cDNA library was constructed in order to identify silkworm PM genes. The capacity of the initial library was 6.92 × 10(6) pfu/ml, along with a recombination rate of 92.14% and a postamplification titer of 4.10 × 10(9) pfu/ml. Three silkworm PM protein genes were obtained by immunoscreening, two of which were chitin-binding protein (CBP) genes and one of which was a chitin deacetylase (CDA) gene as revealed by sequence analysis. Three genes were named BmCBP02, BmCBP13, and BmCDA17, and their ORF sizes are 678, 1,029, and 645 bp, respectively; all of them contain sequences of chitin-binding domains. Phylogenetic analysis indicated that BmCBP02 has the highest consensus with Mamestra configurata CBP at 61.0%; BmCBP13 has the highest consensus with Loxostege sticticalis PM CBP at 53.35%; BmCDA17 has the highest consensus with Helicoverpa armigera CDA5a at 70.83%. Tissue transcriptional analysis revealed that all three genes were specifically expressed in the midgut, and during the developmental process of fifth-instar silkworms, the transcription of all the genes showed an upward trend. This study laid a foundation for further studies on the functions of silkworm PM genes.

  8. De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries

    PubMed Central

    Cho, Namjin; Hwang, Byungjin; Yoon, Jung-ki; Park, Sangun; Lee, Joongoo; Seo, Han Na; Lee, Jeewon; Huh, Sunghoon; Chung, Jinsoo; Bang, Duhee

    2015-01-01

    Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants. PMID:26387459

  9. [Construction of root library by SSH and preliminary analysis of genes responsible for phosphorus deficiency in maize].

    PubMed

    Huang, Q; Gao, S B; Zhang, Z M; Lin, H J; Pan, G T; Yang, K C; Rong, T Z

    2010-12-01

    An elite maize inbred line with high tolerance to low phosphorus, 178, was studied for constructing root library and analyzing some genes closely related to phosphorus (P) deficiency using SSH and Semi-quantitative RT-PCR. As a result, 3648 preliminary clones were obtained for root library under stress of P deficiency. By DNA sequencing of 34 random clones, we obtained 23 unique EST sequences which are involved in functions of root cell structure, tolerance and defense, protein modification and composition, transcription regulation, metabolism, and other unknown aspects. Five representative genes were further analyzed for their expression models. The results suggested that the molecular mechanism to adapt P deficiency in maize, performed by multi-genes with different contributions, is similar to rice, Arabidopsis and soybean. The expression order of 5 low P tolerant genes in maize root was PAP, GCS, TOM, PDI and AIP. And it was considered preliminarily that physiological and biochemical changes were prior to morphologic changes in maize root and the essential tolerance to low P may be determined by extending absorption of P to wide soil range through adaption of root architecture and root secretions, which is the greatest difference between tolerant and sensitive maize varieties under low P stress.

  10. Rapid screening of an ordered fosmid library to clone multiple polyketide synthase genes of the phytopathogenic fungus Cladosporium phlei.

    PubMed

    So, Kum-Kang; Kim, Jung-Mi; Nguyen, Ngoc-Luong; Park, Jin-Ah; Kim, Beom-Tae; Park, Seung-Moon; Hwang, Ki-Jun; Kim, Dae-Hyuk

    2012-12-01

    In previous studies, the biological characteristics of the fungus Cladosporium phlei and its genetic manipulation by transformation were assessed to improve production of the fungal pigment, phleichrome, which is a fungal perylenequinone that plays an important role in the production of a photodynamic therapeutic agent. However, the low production of this metabolite by the wild-type strain has limited its application. Thus, we attempted to clone and characterize the genes that encode polyketide synthases (PKS), which are responsible for the synthesis of fungal pigments such as perylenequinones including phleichrome, elsinochrome and cercosporin. Thus, we performed genomic DNA PCR using 11 different combinations of degenerate primers targeting conserved domains including β-ketoacyl synthase and acyltransferase domains. Sequence comparison of the PCR amplicons revealed a high homology to known PKSs, and four different PKS genes showing a high similarity to three representative types of PKS genes were amplified. To obtain full-length PKS genes, an ordered gene library of a phleichrome-producing C. phlei strain (ATCC 36193) was constructed in a fosmid vector and 4800 clones were analyzed using a simple pyramidal arrangement system. This hierarchical clustering method combines the efficiency of PCR with enhanced specificity. Among the three representative types of PKSs, two reducing, one partially reducing, and one non-reducing PKS were identified. These genes were subsequently cloned, sequenced, and characterized. Biological characterization of these genes to determine their roles in phleichrome production is underway, with the ultimate aim of engineering this pathway to overproduce the desired substance.

  11. Identification of expressed genes during compatible interaction between stripe rust (Puccinia striiformis) and wheat using a cDNA library

    PubMed Central

    2009-01-01

    Background Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. To establish compatibility with the host, Pst forms special infection structures to invade the plant with minimal damage to host cells. Although compatible interaction between wheat and Pst has been studied using various approaches, research on molecular mechanisms of the interaction is limited. The aim of this study was to develop an EST database of wheat infected by Pst in order to determine transcription profiles of genes involved in compatible wheat-Pst interaction. Results Total RNA, extracted from susceptible infected wheat leaves harvested at 3, 5 and 8 days post inoculation (dpi), was used to create a cDNA library, from which 5,793 ESTs with high quality were obtained and clustered into 583 contigs and 2,160 singletons to give a set of 2,743 unisequences (GenBank accessions: GR302385 to GR305127). The BLASTx program was used to search for homologous genes of the unisequences in the GenBank non-redundant protein database. Of the 2,743 unisequences, 52.8% (the largest category) were highly homologous to plant genes; 16.3% to fungal genes and 30% of no-hit. The functional classification of all ESTs was established based on the database entry giving the best E-value using the Bevan's classification categories. About 50% of the ESTs were significantly homologous to genes encoding proteins with known functions; 20% were similar to genes encoding proteins with unknown functions and 30% did not have significant homology to any sequence in the database. The quantitative real-time PCR (qRT-PCR) analysis determined the transcription profiles and their involvement in the wheat-Pst interaction for seven of the gene. Conclusion The cDNA library is useful for identifying the functional genes involved in the wheat-Pst compatible interaction, and established a new database for studying Pst pathogenesis genes and wheat defense genes

  12. Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries.

    PubMed

    Bouhajja, E; McGuire, M; Liles, M R; Bataille, G; Agathos, S N; George, I F

    2017-01-01

    The microbial potential for toluene degradation within sediments from a tar oil-contaminated site in Flingern, Germany, was assessed using a metagenomic approach. High molecular weight environmental DNA from contaminated sediments was extracted, purified, and cloned into fosmid and BAC vectors and transformed into Escherichia coli. The fosmid library was screened by hybridization with a PCR amplicon of the α-subunit of the toluene 4-monooxygenase gene to identify genes and pathways encoding toluene degradation. Fourteen clones were recovered from the fosmid library, among which 13 were highly divergent from known tmoA genes and several had the closest relatives among Acinetobacter species. The BAC library was transferred to the heterologous hosts Cupriavidus metallidurans (phylum Proteobacteria) and Edaphobacter aggregans (phylum Acidobacteria). The resulting libraries were screened for expression of toluene degradation in the non-degradative hosts. From expression in C. metallidurans, three novel toluene monooxygenase-encoding operons were identified that were located on IncP1 plasmids. The E. aggregans-hosted BAC library led to the isolation of a cloned genetic locus putatively derived from an Acidobacteria taxon that contained genes involved in aerobic and anaerobic toluene degradation. These data suggest the important role of plasmids in the spread of toluene degradative capacity and indicate putative novel tmoA genes present in this hydrocarbon-polluted environment.

  13. A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila.

    PubMed

    Nagarkar-Jaiswal, Sonal; Lee, Pei-Tseng; Campbell, Megan E; Chen, Kuchuan; Anguiano-Zarate, Stephanie; Gutierrez, Manuel Cantu; Busby, Theodore; Lin, Wen-Wen; He, Yuchun; Schulze, Karen L; Booth, Benjamin W; Evans-Holm, Martha; Venken, Koen J T; Levis, Robert W; Spradling, Allan C; Hoskins, Roger A; Bellen, Hugo J

    2015-03-31

    Here, we document a collection of ∼7434 MiMIC (Minos Mediated Integration Cassette) insertions of which 2854 are inserted in coding introns. They allowed us to create a library of 400 GFP-tagged genes. We show that 72% of internally tagged proteins are functional, and that more than 90% can be imaged in unfixed tissues. Moreover, the tagged mRNAs can be knocked down by RNAi against GFP (iGFPi), and the tagged proteins can be efficiently knocked down by deGradFP technology. The phenotypes associated with RNA and protein knockdown typically correspond to severe loss of function or null mutant phenotypes. Finally, we demonstrate reversible, spatial, and temporal knockdown of tagged proteins in larvae and adult flies. This new strategy and collection of strains allows unprecedented in vivo manipulations in flies for many genes. These strategies will likely extend to vertebrates.

  14. A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila

    SciTech Connect

    Nagarkar-Jaiswal, Sonal; Lee, Pei-Tseng; Campbell, Megan E.; Chen, Kuchuan; Anguiano-Zarate, Stephanie; Cantu Gutierrez, Manuel; Busby, Theodore; Lin, Wen-Wen; He, Yuchun; Schulze, Karen L.; Booth, Benjamin W.; Evans-Holm, Martha; Venken, Koen J.T.; Levis, Robert W.; Spradling, Allan C.; Hoskins, Roger A.; Bellen, Hugo J.

    2015-03-31

    Here, we document a collection of ~7434 MiMIC (Minos Mediated Integration Cassette) insertions of which 2854 are inserted in coding introns. They allowed us to create a library of 400 GFP-tagged genes. We show that 72% of internally tagged proteins are functional, and that more than 90% can be imaged in unfixed tissues. Moreover, the tagged mRNAs can be knocked down by RNAi against GFP (iGFPi), and the tagged proteins can be efficiently knocked down by deGradFP technology. The phenotypes associated with RNA and protein knockdown typically correspond to severe loss of function or null mutant phenotypes. Finally, we demonstrate reversible, spatial, and temporal knockdown of tagged proteins in larvae and adult flies. This new strategy and collection of strains allows unprecedented in vivo manipulations in flies for many genes. These strategies will likely extend to vertebrates.

  15. A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila

    DOE PAGES

    Nagarkar-Jaiswal, Sonal; Lee, Pei-Tseng; Campbell, Megan E.; ...

    2015-03-31

    Here, we document a collection of ~7434 MiMIC (Minos Mediated Integration Cassette) insertions of which 2854 are inserted in coding introns. They allowed us to create a library of 400 GFP-tagged genes. We show that 72% of internally tagged proteins are functional, and that more than 90% can be imaged in unfixed tissues. Moreover, the tagged mRNAs can be knocked down by RNAi against GFP (iGFPi), and the tagged proteins can be efficiently knocked down by deGradFP technology. The phenotypes associated with RNA and protein knockdown typically correspond to severe loss of function or null mutant phenotypes. Finally, we demonstratemore » reversible, spatial, and temporal knockdown of tagged proteins in larvae and adult flies. This new strategy and collection of strains allows unprecedented in vivo manipulations in flies for many genes. These strategies will likely extend to vertebrates.« less

  16. Identification of polybacterial communities in patients with postoperative, posttraumatic, and endogenous endophthalmitis through 16S rRNA gene libraries.

    PubMed

    Jayasudha, Rajagopalaboopathi; Narendran, Venkatapathy; Manikandan, Palanisamy; Prabagaran, Solai Ramatchandirane

    2014-05-01

    Endophthalmitis is a potential vision-threatening complication following surgical procedures (postoperative endophthalmitis [POE]), trauma (posttraumatic endophthalmitis [PTE]), and bacteremic seeding of the eye from a distant infection site (endogenous endophthalmitis [EE]). Several studies have revealed the polybacterial characteristics of endophthalmitis, which make the administration of antibiotics to treat the disease challenging. However, until now, the polybacterial communities of POE, PTE, and EE have not been precisely studied. Hence, the present study was designed to identify the bacterial community of endophthalmitis through 16S rRNA gene libraries. Of the 40 intraocular samples tested, 30 libraries were constructed with bacterial nested-PCR-positive samples. The obtained recombinant clones were screened through amplified rRNA gene restriction analysis (ARDRA) to identify unique clones. The multiple types of ARDRA patterns (P=0.345) and diverse bacterial sequences (P=0.277) within the libraries revealed the polybacterial nature of infection in POE, PTE, and EE. Moreover, to the best of our knowledge, this is the first report on polybacterial infection in EE. Gram-positive bacteria, including Bacillus spp. (n=19), Streptococcus spp. (n=18), Staphylococcus spp. (n=6), Exiguobacterium spp. (n=3), Gemella spp. (n=2), Enterococcus spp. (n=2), a Lysinibacillus sp. (n=1), a Clostridium sp. (n=1), and a Nocardia sp. (n=1), and Gram-negative bacteria, including Serratia spp. (n=18), Pseudomonas spp. (n=10), Enterobacter spp. (n=8), Acinetobacter spp. (n=3), Pantoea spp. (n=3), a Haemophilus sp. (n=1), and a Massilia sp. (n=1), were identified. Interestingly, among them, 10 bacterial species were not previously reported to be associated with endophthalmitis or other ocular infections. Besides, the presence of 4 unidentifiable clones suggests the possibility of novel organisms that might cause eye infections. Therefore, it is recommended that, in addition to the

  17. Cloning and functional characterization of endo-β-1,4-glucanase gene from metagenomic library of vermicompost.

    PubMed

    Yasir, Muhammad; Khan, Haji; Azam, Syed Sikander; Telke, Amar; Kim, Seon Won; Chung, Young Ryun

    2013-06-01

    In the vermicomposting of paper mill sludge, the activity of earthworms is very dependent on dietetic polysaccharides including cellulose as energy sources. Most of these polymers are degraded by the host microbiota and considered potentially important source for cellulolytic enzymes. In the present study, a metagenomic library was constructed from vermicompost (VC) prepared with paper mill sludge and dairy sludge (fresh sludge, FS) and functionally screened for cellulolytic activities. Eighteen cellulase expressing clones were isolated from about 89,000 fosmid clones libraries. A short fragment library was constructed from the most active positive clone (cMGL504) and one open reading frame (ORF) of 1,092 bp encoding an endo-β-1,4-glucanase was indentified which showed 88% similarity with Cellvibrio mixtus cellulase A gene. The endo-β-1,4-glucanase cmgl504 gene was overexpressed in Escherichia coli. The purified recombinant cmgl504 cellulase displayed activities at a broad range of temperature (25-55°C) and pH (5.5-8.5). The enzyme degraded carboxymethyl cellulose (CMC) with 15.4 U, while having low activity against avicel. No detectable activity was found for xylan and laminarin. The enzyme activity was stimulated by potassium chloride. The deduced protein and three-dimensional structure of metagenome-derived cellulase cmgl504 possessed all features, including general architecture, signature motifs, and N-terminal signal peptide, followed by the catalytic domain of cellulase belonging to glycosyl hydrolase family 5 (GHF5). The cellulases cloned in this work may play important roles in the degradation of celluloses in vermicomposting process and could be exploited for industrial application in future.

  18. The Identification of Genes Important in Pseudomonas syringae pv. phaseolicola Plant Colonisation Using In Vitro Screening of Transposon Libraries.

    PubMed

    Manoharan, Bharani; Neale, Helen C; Hancock, John T; Jackson, Robert W; Arnold, Dawn L

    2015-01-01

    The bacterial plant pathogen Pseudomonas syringae pv. phaseolicola (Pph) colonises the surface of common bean plants before moving into the interior of plant tissue, via wounds and stomata. In the intercellular spaces the pathogen proliferates in the apoplastic fluid and forms microcolonies (biofilms) around plant cells. If the pathogen can suppress the plant's natural resistance response, it will cause halo blight disease. The process of resistance suppression is fairly well understood, but the mechanisms used by the pathogen in colonisation are less clear. We hypothesised that we could apply in vitro genetic screens to look for changes in motility, colony formation, and adhesion, which are proxies for infection, microcolony formation and cell adhesion. We made transposon (Tn) mutant libraries of Pph strains 1448A and 1302A and found 106/1920 mutants exhibited alterations in colony morphology, motility and biofilm formation. Identification of the insertion point of the Tn identified within the genome highlighted, as expected, a number of altered motility mutants bearing mutations in genes encoding various parts of the flagellum. Genes involved in nutrient biosynthesis, membrane associated proteins, and a number of conserved hypothetical protein (CHP) genes were also identified. A mutation of one CHP gene caused a positive increase in in planta bacterial growth. This rapid and inexpensive screening method allows the discovery of genes important for in vitro traits that can be correlated to roles in the plant interaction.

  19. The Identification of Genes Important in Pseudomonas syringae pv. phaseolicola Plant Colonisation Using In Vitro Screening of Transposon Libraries

    PubMed Central

    Hancock, John T.; Jackson, Robert W.; Arnold, Dawn L.

    2015-01-01

    The bacterial plant pathogen Pseudomonas syringae pv. phaseolicola (Pph) colonises the surface of common bean plants before moving into the interior of plant tissue, via wounds and stomata. In the intercellular spaces the pathogen proliferates in the apoplastic fluid and forms microcolonies (biofilms) around plant cells. If the pathogen can suppress the plant’s natural resistance response, it will cause halo blight disease. The process of resistance suppression is fairly well understood, but the mechanisms used by the pathogen in colonisation are less clear. We hypothesised that we could apply in vitro genetic screens to look for changes in motility, colony formation, and adhesion, which are proxies for infection, microcolony formation and cell adhesion. We made transposon (Tn) mutant libraries of Pph strains 1448A and 1302A and found 106/1920 mutants exhibited alterations in colony morphology, motility and biofilm formation. Identification of the insertion point of the Tn identified within the genome highlighted, as expected, a number of altered motility mutants bearing mutations in genes encoding various parts of the flagellum. Genes involved in nutrient biosynthesis, membrane associated proteins, and a number of conserved hypothetical protein (CHP) genes were also identified. A mutation of one CHP gene caused a positive increase in in planta bacterial growth. This rapid and inexpensive screening method allows the discovery of genes important for in vitro traits that can be correlated to roles in the plant interaction. PMID:26325299

  20. Screening and characterization of a novel cellulase gene from the gut microflora of Hermetia illucens using metagenomic library.

    PubMed

    Lee, Chang-Muk; Lee, Young-Seok; Seo, So-Hyeon; Yoon, Sang-Hong; Kim, Soo-Jin; Hahn, Bum-Soo; Sim, Joon-Soo; Koo, Bon-Sung

    2014-09-01

    A metagenomic fosmid library was constructed using genomic DNA isolated from the gut microflora of Hermetia illucens, a black soldier fly. A cellulase-positive clone, with the CS10 gene, was identified by extensive Congo-red overlay screenings for cellulase activity from the fosmid library of 92,000 clones. The CS10 gene was composed of a 996 bp DNA sequence encoding the mature protein of 331 amino acids. The deduced amino acids of CS10 showed 72% sequence identity with the glycosyl hydrolase family 5 gene of Dysgonomonas mossii, displaying no significant sequence homology to already known cellulases. The purified CS10 protein presented a single band of cellulase activity with a molecular mass of approximately 40 kDa on the SDS-PAGE gel and zymogram. The purified CS10 protein exhibited optimal activity at 50°C and pH 7.0, and the thermostability and pH stability of CS10 were preserved at the ranges of 20~50°C and pH 4.0~10.0. CS10 exhibited little loss of cellulase activity against various chemical reagents such as 10% polar organic solvents, 1% non-ionic detergents, and 0.5 M denaturing agents. Moreover, the substrate specificity and the product patterns by thinlayer chromatography suggested that CS10 is an endo-β-1,4-glucanase. From these biochemical properties of CS10, it is expected that the enzyme has the potential for application in industrial processes.

  1. Mammalian cDNA Library from the NIH Mammalian Gene Collection (MGC) | Office of Cancer Genomics

    Cancer.gov

    The MGC provides the research community full-length clones for most of the defined (as of 2006) human and mouse genes, along with selected clones of cow and rat genes. Clones were designed to allow easy transfer of the ORF sequences into nearly any type of expression vector. MGC provides protein ‘expression-ready’ clones for each of the included human genes. MGC is part of the ORFeome Collaboration (OC).

  2. 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,…

  3. Facile Construction of Random Gene Mutagenesis Library for Directed Evolution Without the Use of Restriction Enzyme in Escherichia coli.

    PubMed

    Kim, Jae-Eung; Huang, Rui; Chen, Hui; You, Chun; Zhang, Y-H Percival

    2016-09-01

    A foolproof protocol was developed for the construction of mutant DNA library for directed protein evolution. First, a library of linear mutant gene was generated by error-prone PCR or molecular shuffling, and a linear vector backbone was prepared by high-fidelity PCR. Second, the amplified insert and vector fragments were assembled by overlap-extension PCR with a pair of 5'-phosphorylated primers. Third, full-length linear plasmids with phosphorylated 5'-ends were self-ligated with T4 ligase, yielding circular plasmids encoding mutant variants suitable for high-efficiency transformation. Self-made competent Escherichia coli BL21(DE3) showed a transformation efficiency of 2.4 × 10(5) cfu/µg of the self-ligated circular plasmid. Using this method, three mutants of mCherry fluorescent protein were found to alter their colors and fluorescent intensities under visible and UV lights, respectively. Also, one mutant of 6-phosphorogluconate dehydrogenase from a thermophilic bacterium Moorella thermoacetica was found to show the 3.5-fold improved catalytic efficiency (kcat /Km ) on NAD(+) as compared to the wild-type. This protocol is DNA-sequence independent, and does not require restriction enzymes, special E. coli host, or labor-intensive optimization. In addition, this protocol can be used for subcloning the relatively long DNA sequences into any position of plasmids.

  4. Identification of Novel Genes Affected by Gamma Irradiation Using a Gene-Trapped Library of Human Mammary Epithelial Cells

    DTIC Science & Technology

    2005-04-01

    Chromosomal and chromatid analysis was performed on the DREV 1 knockdown MCF10A cells to access cel l survival following ionizing radiation treatment...statement of work as well as their response to ionizing radiation . 14 . SUBJECT TERMS 15 . NUMBER OF PAGE S 3 0 Gamma Irradiation, gene trapping...line with and without ionizing radiation treatment . We felt that it was important t o analyze the identified gene expression levels following IR

  5. Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes.

    PubMed

    Coyne, C J; McClendon, M T; Walling, J G; Timmerman-Vaughan, G M; Murray, S; Meksem, K; Lightfoot, D A; Shultz, J L; Keller, K E; Martin, R R; Inglis, D A; Rajesh, P N; McPhee, K E; Weeden, N F; Grusak, M A; Li, C-M; Storlie, E W

    2007-09-01

    Pea (Pisum sativum L.) has a genome of about 4 Gb that appears to share conserved synteny with model legumes having genomes of 0.2-0.4 Gb despite extensive intergenic expansion. Pea plant inventory (PI) accession 269818 has been used to introgress genetic diversity into the cultivated germplasm pool. The aim here was to develop pea bacterial artificial chromosome (BAC) libraries that would enable the isolation of genes involved in plant disease resistance or control of economically important traits. The BAC libraries encompassed about 3.2 haploid genome equivalents consisting of partially HindIII-digested DNA fragments with a mean size of 105 kb that were inserted in 1 of 2 vectors. The low-copy oriT-based T-DNA vector (pCLD04541) library contained 55 680 clones. The single-copy oriS-based vector (pIndigoBAC-5) library contained 65 280 clones. Colony hybridization of a universal chloroplast probe indicated that about 1% of clones in the libraries were of chloroplast origin. The presence of about 0.1% empty vectors was inferred by white/blue colony plate counts. The usefulness of the libraries was tested by 2 replicated methods. First, high-density filters were probed with low copy number sequences. Second, BAC plate-pool DNA was used successfully to PCR amplify 7 of 9 published pea resistance gene analogs (RGAs) and several other low copy number pea sequences. Individual BAC clones encoding specific sequences were identified. Therefore, the HindIII BAC libraries of pea, based on germplasm accession PI 269818, will be useful for the isolation of genes underlying disease resistance and other economically important traits.

  6. Analysis of microbiota associated with peri-implantitis using 16S rRNA gene clone library

    PubMed Central

    Koyanagi, Tatsuro; Sakamoto, Mitsuo; Takeuchi, Yasuo; Ohkuma, Moriya; Izumi, Yuichi

    2010-01-01

    Background Peri-implantitis (PI) is an inflammatory disease which leads to the destruction of soft and hard tissues around osseointegrated implants. The subgingival microbiota appears to be responsible for peri-implant lesions and although the complexity of the microbiota has been reported in PI, the microbiota responsible for PI has not been identified. Objective The purpose of this study was to identify the microbiota in subjects who have PI, clinically healthy implants, and periodontitis-affected teeth using 16S rRNA gene clone library analysis to clarify the microbial differences. Design Three subjects participated in this study. The conditions around the teeth and implants were evaluated based on clinical and radiographic examinations and diseased implants, clinically healthy implants, and periodontally diseased teeth were selected. Subgingival plaque samples were taken from the deepest pockets using sterile paper points. Prevalence and identity of bacteria was analyzed using a 16S rRNA gene clone library technique. Results A total of 112 different species were identified from 335 clones sequenced. Among the 112 species, 51 (46%) were uncultivated phylotypes, of which 22 were novel phylotypes. The numbers of bacterial species identified at the sites of PI, periodontitis, and periodontally healthy implants were 77, 57, and 12, respectively. Microbiota in PI mainly included Gram-negative species and the composition was more diverse when compared to that of the healthy implant and periodontitis. The phyla Chloroflexi, Tenericutes, and Synergistetes were only detected at PI sites, as were Parvimonas micra, Peptostreptococcus stomatis, Pseudoramibacter alactolyticus, and Solobacterium moorei. Low levels of periodontopathic bacteria, such as Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, were seen in peri-implant lesions. Conclusions The biofilm in PI showed a more complex microbiota when compared to periodontitis and periodontally healthy teeth

  7. Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp.

    PubMed Central

    Xu, Min; Wang, Yemin; Zhao, Zhilong; Gao, Guixi; Huang, Sheng-Xiong; Kang, Qianjin; He, Xinyi; Lin, Shuangjun; Pang, Xiuhua; Deng, Zixin

    2016-01-01

    ABSTRACT Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in Streptomyces spp. We demonstrate mining from a strain of Streptomyces rochei, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host Streptomyces lividans SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from S. rochei. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways. IMPORTANCE Microbial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from Streptomyces. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including

  8. Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening.

    PubMed

    Yang, J H; Ye, J H; Wallace, D C

    1984-01-11

    We present a computer program, FINPROBE, which utilizes known amino acid sequence data to deduce minimum redundancy oligonucleotide probes for use in screening cDNA or genomic libraries or in primer extension. The user enters the amino acid sequence of interest, the desired probe length, the number of probes sought, and the constraints on oligonucleotide synthesis. The computer generates a table of possible probes listed in increasing order of redundancy and provides the location of each probe in the protein and mRNA coding sequence. Activation of a next function provides the amino acid and mRNA sequences of each probe of interest as well as the complementary sequence and the minimum dissociation temperature of the probe. A final routine prints out the amino acid sequence of the protein in parallel with the mRNA sequence listing all possible codons for each amino acid.

  9. 16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development - Poster

    EPA Science Inventory

    We examined the bacterial composition of chlorinated drinking water using 16S rRNA gene clone libraries derived from RNA and DNA extracted from twelve water samples collected in three different months (June, August, and September of 2007). Phylogenetic analysis of 1234 and 1117 ...

  10. 16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development

    EPA Science Inventory

    We examined the bacterial composition of chlorinated drinking water using 16S rRNA gene clone libraries derived from RNA and DNA extracted from twelve water samples collected in three different months (June, August, and September of 2007). Phylogenetic analysis of 1234 and 1117 ...

  11. Generation of a Genome Scale Lentiviral Vector Library for EF1α Promoter-Driven Expression of Human ORFs and Identification of Human Genes Affecting Viral Titer

    PubMed Central

    Škalamera, Dubravka; Dahmer, Mareike; Purdon, Amy S.; Wilson, Benjamin M.; Ranall, Max V.; Blumenthal, Antje; Gabrielli, Brian; Gonda, Thomas J.

    2012-01-01

    The bottleneck in elucidating gene function through high-throughput gain-of-function genome screening is the limited availability of comprehensive libraries for gene overexpression. Lentiviral vectors are the most versatile and widely used vehicles for gene expression in mammalian cells. Lentiviral supernatant libraries for genome screening are commonly generated in the HEK293T cell line, yet very little is known about the effect of introduced sequences on the produced viral titer, which we have shown to be gene dependent. We have generated an arrayed lentiviral vector library for the expression of 17,030 human proteins by using the GATEWAY® cloning system to transfer ORFs from the Mammalian Gene Collection into an EF1alpha promoter-dependent lentiviral expression vector. This promoter was chosen instead of the more potent and widely used CMV promoter, because it is less prone to silencing and provides more stable long term expression. The arrayed lentiviral clones were used to generate viral supernatant by packaging in the HEK293T cell line. The efficiency of transfection and virus production was estimated by measuring the fluorescence of IRES driven GFP, co-expressed with the ORFs. More than 90% of cloned ORFs produced sufficient virus for downstream screening applications. We identified genes which consistently produced very high or very low viral titer. Supernatants from select clones that were either high or low virus producers were tested on a range of cell lines. Some of the low virus producers, including two previously uncharacterized proteins were cytotoxic to HEK293T cells. The library we have constructed presents a powerful resource for high-throughput gain-of-function screening of the human genome and drug-target discovery. Identification of human genes that affect lentivirus production may lead to improved technology for gene expression using lentiviral vectors. PMID:23251614

  12. The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms

    PubMed Central

    Tanino, Motohiko; Debily, Marie-Anne; Tamura, Takuro; Hishiki, Teruyoshi; Ogasawara, Osamu; Murakawa, Katsuji; Kawamoto, Shoko; Itoh, Kouichi; Watanabe, Shinya; de Souza, Sandro José; Imbeaud, Sandrine; Graudens, Esther; Eveno, Eric; Hilton, Phillip; Sudo, Yukio; Kelso, Janet; Ikeo, Kazuho; Imanishi, Tadashi; Gojobori, Takashi; Auffray, Charles; Hide, Winston; Okubo, Kousaku

    2005-01-01

    The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein expression data from multiple platforms that has been associated with both manually annotated full-length cDNAs from H-InvDB and RefSeq sequences. Of the H-Inv predicted genes, 18 897 have associated expression data generated by at least one platform. H-ANGEL utilizes categorized mRNA expression data from both publicly available and proprietary sources. It incorporates data generated by three types of methods from seven different platforms. The data are provided to the user in the form of a web-based viewer with numerous query options. H-ANGEL is updated with each new release of cDNA and genome sequence build. In future editions, we will incorporate the capability for expression data updates from existing and new platforms. H-ANGEL is accessible at http://www.jbirc.aist.go.jp/hinv/h-angel/. PMID:15608263

  13. Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays

    PubMed Central

    Mahalingam, Ramamurthy; Fedoroff, Nina

    2001-01-01

    We describe a method to screen pools of DNA from multiple transposon lines for insertions in many genes simultaneously. We use thermal asymmetric interlaced–PCR, a hemispecific PCR amplification protocol that combines nested, insertion-specific primers with degenerate primers, to amplify DNA flanking the transposons. In reconstruction experiments with previously characterized Arabidopsis lines carrying insertions of the maize Dissociation (Ds) transposon, we show that fluorescently labeled, transposon-flanking fragments overlapping ORFs hybridize to cognate expressed sequence tags (ESTs) on a DNA microarray. We further show that insertions can be detected in DNA pools from as many as 100 plants representing different transposon lines and that all of the tested, transposon-disrupted genes whose flanking fragments can be amplified individually also can be detected when amplified from the pool. The ability of a transposon-flanking fragment to hybridize declines rapidly with decreasing homology to the spotted DNA fragment, so that only ESTs with >90% homology to the transposon-disrupted gene exhibit significant cross-hybridization. Because thermal asymmetric interlaced–PCR fragments tend to be short, use of the present method favors recovery of insertions in and near genes. We apply the technique to screening pools of new Ds lines using cDNA microarrays containing ESTs for ≈1,000 stress-induced and -repressed Arabidopsis genes. PMID:11416215

  14. Identification of New Genes Contributing to the Extreme Radioresistance of Deinococcus radiodurans Using a Tn5-Based Transposon Mutant Library

    PubMed Central

    Passot, Fanny; Dutertre, Murielle; Porteron, Martine; Confalonieri, Fabrice; Sommer, Suzanne; Pasternak, Cécile

    2015-01-01

    Here, we have developed an extremely efficient in vivo Tn5-based mutagenesis procedure to construct a Deinococcus radiodurans insertion mutant library subsequently screened for sensitivity to genotoxic agents such as γ and UV radiations or mitomycin C. The genes inactivated in radiosensitive mutants belong to various functional categories, including DNA repair functions, stress responses, signal transduction, membrane transport, several metabolic pathways, and genes of unknown function. Interestingly, preliminary characterization of previously undescribed radiosensitive mutants suggests the contribution of cyclic di-AMP signaling in the recovery of D. radiodurans cells from genotoxic stresses, probably by modulating several pathways involved in the overall cell response. Our analyses also point out a new transcriptional regulator belonging to the GntR family, encoded by DR0265, and a predicted RNase belonging to the newly described Y family, both contributing to the extreme radioresistance of D. radiodurans. Altogether, this work has revealed new cell responses involved either directly or indirectly in repair of various cell damage and confirmed that D. radiodurans extreme radiation resistance is determined by a multiplicity of pathways acting as a complex network. PMID:25884619

  15. A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila

    PubMed Central

    Nagarkar-Jaiswal, Sonal; Lee, Pei-Tseng; Campbell, Megan E; Chen, Kuchuan; Anguiano-Zarate, Stephanie; Cantu Gutierrez, Manuel; Busby, Theodore; Lin, Wen-Wen; He, Yuchun; Schulze, Karen L; Booth, Benjamin W; Evans-Holm, Martha; Venken, Koen JT; Levis, Robert W; Spradling, Allan C; Hoskins, Roger A; Bellen, Hugo J

    2015-01-01

    Here, we document a collection of ∼7434 MiMIC (Minos Mediated Integration Cassette) insertions of which 2854 are inserted in coding introns. They allowed us to create a library of 400 GFP-tagged genes. We show that 72% of internally tagged proteins are functional, and that more than 90% can be imaged in unfixed tissues. Moreover, the tagged mRNAs can be knocked down by RNAi against GFP (iGFPi), and the tagged proteins can be efficiently knocked down by deGradFP technology. The phenotypes associated with RNA and protein knockdown typically correspond to severe loss of function or null mutant phenotypes. Finally, we demonstrate reversible, spatial, and temporal knockdown of tagged proteins in larvae and adult flies. This new strategy and collection of strains allows unprecedented in vivo manipulations in flies for many genes. These strategies will likely extend to vertebrates. DOI: http://dx.doi.org/10.7554/eLife.05338.001 PMID:25824290

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

    PubMed

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

    2011-01-01

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

  17. Using a suppression subtractive library-based approach to identify tobacco genes regulated in response to short-term sulphur deficit.

    PubMed

    Wawrzyńska, Anna; Lewandowska, Małgorzata; Hawkesford, Malcolm J; Sirko, Agnieszka

    2005-06-01

    Monitoring expression at the transcriptional level is an essential first step for the functional analysis of plant genes. Genes encoding proteins directly involved in sulphur metabolism constitute only a small fraction of all the genes affected by sulphur deficiency stress. Transcriptional responses to various periods of sulphur deprivation have been extensively studied in Arabidopsis thaliana; however, no corresponding data are available for Solanaceae sp. To address this problem, a subtractive library-based approach to search for tobacco genes regulated by a short-term sulphur starvation has been adopted. In this work, 38 genes were identified, of which 22 were regulated positively and 16 were regulated negatively. The transcript levels of the representative genes were monitored in four parts of the plants (mature and immature leaves, stems, and roots), which exhibited differential sulphur deficiency. Interestingly, some genes exhibit different regulation of expression in different parts of the plants. Database analysis allowed assignment of the potential function for many of the identified genes; however, the functions of a small number of genes strongly regulated by sulphur starvation remain unknown. The genes were grouped into nine functional categories, each including both up- and down-regulated genes. The possible links between the identified regulated genes and sulphur metabolism are considered, and compared where possible with expression patterns in Arabidopsis thaliana. Although no obvious regulatory genes were identified, the genes encoding proteins of unknown function remain as potential components of the regulatory processes.

  18. Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages

    PubMed Central

    Zhou, Wen-Zhao; Zhang, Yan-Mei; Lu, Jun-Ying; Li, Jun-Feng

    2012-01-01

    To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing. PMID:23202944

  19. Construction and evaluation of normalized cDNA libraries enriched with full-length sequences for rapid discovery of new genes from Sisal (Agave sisalana Perr.) different developmental stages.

    PubMed

    Zhou, Wen-Zhao; Zhang, Yan-Mei; Lu, Jun-Ying; Li, Jun-Feng

    2012-10-12

    To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing.

  20. Construction of a genomic DNA library with a TA vector and its application in cloning of the phytoene synthase gene from the cyanobacterium Spirulina platensis M-135

    NASA Astrophysics Data System (ADS)

    Yoshikazu, Kawata; Shin-Ichi, Yano; Hiroyuki, Kojima

    1998-03-01

    An efficient and simple method for constructing a genomic DNA library using a TA cloning vector is presented. It is based on the sonicative cleavage of genomic DNA and modification of fragment ends with Taq DNA polymerase, followed by ligation using a TA vector. This method was applied for cloning of the phytoene synthase gene crt B from Spirulina platensis. This method is useful when genomic DNA cannot be efficiently digested with restriction enzymes, a problem often encountered during the construction of a genomic DNA library of cyanobacteria.

  1. Construction of a full-length cDNA library of Solen grandis dunker and identification of defense- and immune-related genes

    NASA Astrophysics Data System (ADS)

    Sun, Guohua; Liu, Xiangquan; Ren, Lihua; Yang, Jianmin; Wei, Xiumei; Yang, Jialong

    2013-11-01

    The basic genetic characteristics, important functional genes, and entire transcriptome of Solen grandis Dunker were investigated by constructing a full-length cDNA library with the `switching mechanism at the 5'-end of the RNA transcript' (SMART) technique. Total RNA was isolated from the immune-relevant tissues, gills and hemocytes, using the Trizol reagent, and cDNA fragments were digested with Sfi I before being ligated to the pBluescript II SK* vector. The cDNA library had a titer of 1048 cfu μL-1 and a storage capacity of 1.05×106 cfu. Approximately 98% of the clones in the library were recombinants, and the fragment lengths of insert cDNA ranged from 0.8 kb to 3.0 kb. A total of 2038 expressed sequence tags were successfully sequenced and clustered into 965 unigenes. BLASTN analysis showed that 240 sequences were highly similar to the known genes (E-value < 1e -5; percent identity >80%), accounting for 25% of the total unigenes. According to the Gene Ontology, these unigenes were related to several biological processes, including cell structure, signal transport, protein synthesis, transcription, energy metabolism, and immunity. Fifteen of the identified sequences were related to defense and immunity. The full-length cDNA sequence of HSC70 was obtained. The cDNA library of S. grandis provided a useful resource for future researches of functional genomics related to stress tolerance, immunity, and other physiological activities.

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

    PubMed Central

    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

  3. Analysis of Two Complementary Single-Gene Deletion Mutant Libraries of Salmonella Typhimurium in Intraperitoneal Infection of BALB/c Mice.

    PubMed

    Silva-Valenzuela, Cecilia A; Molina-Quiroz, Roberto C; Desai, Prerak; Valenzuela, Camila; Porwollik, Steffen; Zhao, Ming; Hoffman, Robert M; Andrews-Polymenis, Helene; Contreras, Inés; Santiviago, Carlos A; McClelland, Michael

    2015-01-01

    Two pools of individual single gene deletion (SGD) mutants of S. Typhimurium 14028s encompassing deletions of 3,923 annotated non-essential ORFs and sRNAs were screened by intraperitoneal (IP) injection in BALB/c mice followed by recovery from spleen and liver 2 days post infection. The relative abundance of each mutant was measured by microarray hybridization. The two mutant libraries differed in the orientation of the antibiotic resistance cassettes (either sense-oriented Kan(R), SGD-K, or antisense-oriented Cam(R), SGD-C). Consistent systemic colonization defects were observed in both libraries and both organs for hundreds of mutants of genes previously reported to be important after IP injection in this animal model, and for about 100 new candidate genes required for systemic colonization. Four mutants with a range of apparent fitness defects were confirmed using competitive infections with the wild-type parental strain: ΔSTM0286, ΔSTM0551, ΔSTM2363, and ΔSTM3356. Two mutants, ΔSTM0286 and ΔSTM2363, were then complemented in trans with a plasmid encoding an intact copy of the corresponding wild-type gene, and regained the ability to fully colonize BALB/c mice systemically. These results suggest the presence of many more undiscovered Salmonella genes with phenotypes in IP infection of BALB/c mice, and validate the libraries for application to other systems.

  4. Analysis of Two Complementary Single-Gene Deletion Mutant Libraries of Salmonella Typhimurium in Intraperitoneal Infection of BALB/c Mice

    PubMed Central

    Silva-Valenzuela, Cecilia A.; Molina-Quiroz, Roberto C.; Desai, Prerak; Valenzuela, Camila; Porwollik, Steffen; Zhao, Ming; Hoffman, Robert M.; Andrews-Polymenis, Helene; Contreras, Inés; Santiviago, Carlos A.; McClelland, Michael

    2016-01-01

    Two pools of individual single gene deletion (SGD) mutants of S. Typhimurium 14028s encompassing deletions of 3,923 annotated non-essential ORFs and sRNAs were screened by intraperitoneal (IP) injection in BALB/c mice followed by recovery from spleen and liver 2 days post infection. The relative abundance of each mutant was measured by microarray hybridization. The two mutant libraries differed in the orientation of the antibiotic resistance cassettes (either sense-oriented KanR, SGD-K, or antisense-oriented CamR, SGD-C). Consistent systemic colonization defects were observed in both libraries and both organs for hundreds of mutants of genes previously reported to be important after IP injection in this animal model, and for about 100 new candidate genes required for systemic colonization. Four mutants with a range of apparent fitness defects were confirmed using competitive infections with the wild-type parental strain: ΔSTM0286, ΔSTM0551, ΔSTM2363, and ΔSTM3356. Two mutants, ΔSTM0286 and ΔSTM2363, were then complemented in trans with a plasmid encoding an intact copy of the corresponding wild-type gene, and regained the ability to fully colonize BALB/c mice systemically. These results suggest the presence of many more undiscovered Salmonella genes with phenotypes in IP infection of BALB/c mice, and validate the libraries for application to other systems. PMID:26779130

  5. Selective enrichment of environmental DNA libraries for genes encoding nonribosomal peptides and polyketides by phosphopantetheine transferase-dependent complementation of siderophore biosynthesis.

    PubMed

    Charlop-Powers, Zachary; Banik, Jacob J; Owen, Jeremy G; Craig, Jeffrey W; Brady, Sean F

    2013-01-18

    The cloning of DNA directly from environmental samples provides a means to functionally access biosynthetic gene clusters present in the genomes of the large fraction of bacteria that remains recalcitrant to growth in the laboratory. Herein, we demonstrate a method by which complementation of phosphopantetheine transferase deletion mutants can be used to restore siderophore biosynthesis and to therefore selectively enrich eDNA libraries for nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene sequences to unprecedented levels. The common use of NRPS/PKS-derived siderophores across bacterial taxa makes this method generalizable and should allow for the facile selective enrichment of NRPS/PKS-containing biosynthetic gene clusters from large environmental DNA libraries using a wide variety of phylogenetically diverse bacterial hosts.

  6. Selective enrichment of environmental DNA libraries for genes encoding nonribosomal peptides and polyketides by phosphopantetheine transferase-dependent complementation of siderophore biosynthesis

    PubMed Central

    Charlop-Powers, Zachary; Banik, Jacob J.; Owen, Jeremy G.; Craig, Jeffrey W.; Brady, Sean F.

    2012-01-01

    The cloning of DNA directly from environmental samples provides a means to functionally access biosynthetic gene clusters present in the genomes of the large fraction of bacteria that remains recalcitrant to growth in the laboratory. Herein we demonstrate a method by which complementation of phosphopantetheine transferase deletion mutants can be used to restore siderophore biosynthesis and to therefore selectively enrich eDNA libraries for nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene sequences to unprecedented levels. The common use of NRPS/PKS-derived siderophores across bacterial taxa makes this method generalizable and should allow for the facile selective enrichment of NRPS/PKS-containing biosynthetic gene clusters from large environmental DNA libraries using a wide variety of phylogenetically diverse bacterial hosts. PMID:23072412

  7. Cloning and identification of novel hydrolase genes from a dairy cow rumen metagenomic library and characterization of a cellulase gene

    PubMed Central

    2012-01-01

    Background Interest in cellulose degrading enzymes has increased in recent years due to the expansion of the cellulosic biofuel industry. The rumen is a highly adapted environment for the degradation of cellulose and a promising source of enzymes for industrial use. To identify cellulase enzymes that may be of such use we have undertaken a functional metagenomic screen to identify cellulase enzymes from the bacterial community in the rumen of a grass-hay fed dairy cow. Results Twenty five clones specifying cellulose activity were identified. Subcloning and sequence analysis of a subset of these hydrolase-positive clones identified 10 endoglucanase genes. Preliminary characterization of the encoded cellulases was carried out using crude extracts of each of the subclones. Zymogram analysis using carboxymethylcellulose as a substrate showed a single positive band for each subclone, confirming that only one functional cellulase gene was present in each. One cellulase gene, designated Cel14b22, was expressed at a high level in Escherichia coli and purified for further characterization. The purified recombinant enzyme showed optimal activity at pH 6.0 and 50°C. It was stable over a broad pH range, from pH 4.0 to 10.0. The activity was significantly enhanced by Mn2+ and dramatically reduced by Fe3+ or Cu2+. The enzyme hydrolyzed a wide range of beta-1,3-, and beta-1,4-linked polysaccharides, with varying activities. Activities toward microcrystalline cellulose and filter paper were relatively high, while the highest activity was toward Oat Gum. Conclusion The present study shows that a functional metagenomic approach can be used to isolate previously uncharacterized cellulases from the rumen environment. PMID:23062472

  8. The analysis of VH and VL genes repertoires of Fab library built from peripheral B cells of human rabies virus vaccinated donors.

    PubMed

    Houimel, Mehdi

    2014-08-01

    A human combinatorial Fab antibody library was generated from immune repertoire based on peripheral B cells of ten rabies virus vaccinated donors. The analysis of random Fab fragments from the unselected library presented some bias of V gene usage towards IGHV-genes and IGLV-gen families. The screening of the Fab library on rabies virus allowed specific human Fab antibody fragments characterized for their gene encoding sequences, binding and specificities to RV. Genetic analysis of selected Fabs indicated that the IGHV and IGLV differ from the germ-line sequence. At the level of nucleotide sequences, the IGHV and IGLV domains were found to share 74-92% and 90-96% homology with sequences encoded by the corresponding human germ-line genes respectively. IGHV domains are characterized most frequently by IGHV3 genes, and large proportions of the anti-RV heavy chain IGHV domains are obtained following a VDJ recombination process that uses IGHD3, IGHD2, IGHD1 and IGHD6 genes. IGHJ3 and IGHJ4 genes are predominantly used in RV-Fab. The IGLV domains are dominated by IGKV1, IGLV1 and IGLV3 genes. Numerous somatic hypermutations in the RV-specific IGHV are detected, but only limited amino acid replacement in most of the RV-specific IGLV particularly in those encoded by J proximal IGLV or IGKV genes are found. Furthermore, IGHV3-IGKV1, IGHV3-IGVL1, and IGHV3-IGLV3 germ-line family pairings are preferentially enriched after the screening on rabies virus.

  9. Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit

    PubMed Central

    Rodrigues, Fabiana Aparecida; Marcolino-Gomes, Juliana; de Fátima Corrêa Carvalho, Josirlei; do Nascimento, Leandro Costa; Neumaier, Norman; Farias, José Renato Bouças; Carazzolle, Marcelo Falsarella; Marcelino, Francismar Corrêa; Nepomuceno, Alexandre Lima

    2012-01-01

    Soybean has a wide range of applications in the industry and, due to its crop potential, its improvement is widely desirable. During drought conditions, soybean crops suffer significant losses in productivity. Therefore, understanding the responses of the soybean under this stress is an effective way of targeting crop improvement techniques. In this study, we employed the Suppressive Subtractive Hybridization (SSH) technique to investigate differentially expressed genes under water deficit conditions. Embrapa 48 and BR 16 soybean lines, known as drought-tolerant and -sensitive, respectively, were grown hydroponically and subjected to different short-term periods of stress by withholding the nutrient solution. Using this approach, we have identified genes expressed during the early response to water deficit in roots and leaves. These genes were compared among the lines to assess probable differences in the plant transcriptomes. In general, similar biochemical processes were predominant in both cultivars; however, there were more considerable differences between roots and leaves of Embrapa 48. Moreover, we present here a fast, clean and straightforward method to obtain drought-stressed root tissues and a large enriched collection of transcripts expressed by soybean plants under water deficit that can be useful for further studies towards the understanding of plant responses to stress. PMID:22802715

  10. Creating Library Spaces: Libraries 2040.

    ERIC Educational Resources Information Center

    Bruijnzeels, Rob

    This paper suggests that by 2004, the traditional public libraries will have ceased to exist and new, attractive future libraries will have taken their place. The Libraries 2040 project of the Netherlands is initiating seven different libraries of the future. The Brabant library is the "ultimate library of the future" for the Dutch…

  11. Delineation of BmSXP antibody V-gene usage from a lymphatic filariasis based immune scFv antibody library.

    PubMed

    Rahumatullah, Anizah; Ahmad, Azimah; Noordin, Rahmah; Lim, Theam Soon

    2015-10-01

    Phage display technology is an important tool for antibody generation or selection. This study describes the development of a scFv library and the subsequent analysis of identified monoclonal antibodies against BmSXP, a recombinant antigen for lymphatic filariasis. The immune library was generated from blood of lymphatic filariasis infected individuals. A TA based intermediary cloning approach was used to increase cloning efficiency for the library construction process. A diverse immune scFv library of 10(8) was generated. Six unique monoclonal antibodies were identified from the 50 isolated clones against BmSXP. Analysis of the clones showed a bias for the IgHV3 and Vκ1 (45.5%) and IgHV2 and Vκ3 (27.3%) gene family. The most favored J segment for light chain is IgKJ1 (45.5%). The most favored D and J segment for heavy chain are IgHD6-13 (75%) and IgHJ3 (47.7%). The information may suggest a predisposition of certain V genes in antibody responses against lymphatic filariasis.

  12. EST library sequencing of genes expressed during early limb regeneration in the fiddler crab and transcriptional responses to ecdysteroid exposure in limb bud explants.

    PubMed

    Durica, David S; Kupfer, Doris; Najar, Fares; Lai, Hongshing; Tang, Yuhong; Griffin, Kathryn; Hopkins, Penny M; Roe, Bruce

    2006-12-01

    We have constructed directional and randomly primed cDNA libraries from mRNAs isolated during progressive stages of fiddler crab (Uca pugilator) limb regeneration. Data from these libraries are being assembled into an on-line database (http://www.genome.ou.edu/crab.html) that is both BLAST and keyword searchable; the data set is also available through GenBank. The first characterized library was made from mRNA isolated 4 days post-autotomy, when the first sign of morphological differentiation, cuticle secretion, is observed. Analysis of 1698 cDNA clones led to assignment of 473 contigs and 417 singlets, for a total of 890 sequences. Of these, ∼86% showed no assignments to characterized genes on database searching, while 14% could be assigned to a known ortholog in the COG (Clusters of Orthologous Groups) database. BLAST searches to specific protein domains in the Gene Ontology database led to assignments for ∼40% of the assembled sequences. Sequence similarity searches of other crustacean EST databases produced hits to 13-30% of the Uca query sequences. The ESTs include several genes that may be potentially ecdysteroid-responsive, such as homologs to chaperone proteins and cuticle protein genes, as well as homologs to arthropod proteins involved in retinoid/terpenoid metabolism. We have tested 3 potential candidate genes for their ability to be induced by ecdysteroid in limb bud explants; an arthropodial cuticle protein gene, and the nuclear receptor genes EcR and RXR. A subset of early blastemal limb buds (8 days post autotomy) show a positive response to ecdysteroid by 1-1.5 h, followed by a decrease in transcript abundance at longer periods of sustained incubation. Later stage buds (12 days post autotomy-late premolt) show decreases in steady-state mRNA levels by 1.5 h, or are completely refractory to ecdysteroid exposure.

  13. Third-Generation Sequencing and Analysis of Four Complete Pig Liver Esterase Gene Sequences in Clones Identified by Screening BAC Library

    PubMed Central

    Zhou, Qiongqiong; Sun, Wenjuan; Liu, Xiyan; Wang, Xiliang; Xiao, Yuncai; Bi, Dingren; Yin, Jingdong; Shi, Deshi

    2016-01-01

    Aim Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing. Methods After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification. Specific primers were then selected based on the PCR amplification results. A three-step PCR screening method was used to identify PLE-positive clones by screening a Rongchang pig BAC library and PacBio third-generation sequencing was performed. BLAST comparisons and other bioinformatics methods were applied for sequence analysis. Results Five PLE-positive BAC clones, designated BAC-10, BAC-70, BAC-75, BAC-119 and BAC-206, were identified. Sequence analysis yielded the complete sequences of four PLE genes, PLE1, PLE-B9, PLE-C4, and PLE-G2. Complete PLE gene sequences were defined as those containing regulatory sequences, exons, and introns. It was found that, not only did the PLE exon sequences of the four genes show a high degree of homology, but also that the intron sequences were highly similar. Additionally, the regulatory region of the genes contained two 720bps reverse complement sequences that may have an important function in the regulation of PLE gene expression. Significance This is the first report to confirm the complete sequences of four PLE genes. In addition, the study demonstrates that each PLE isoform is encoded by a single gene and that the various genes exhibit a high degree of sequence homology, suggesting that the PLE family evolved from a single ancestral gene. Obtaining the complete sequences of these PLE genes

  14. Construction of a genomic library of the food spoilage yeast Zygosaccharomyces bailii and isolation of the beta-isopropylmalate dehydrogenase gene (ZbLEU2).

    PubMed

    Rodrigues, F; Zeeman, A M; Alves, C; Sousa, M J; Steensma, H Y; Côrte-Real, M; Leão, C

    2001-04-01

    A genomic library of the yeast Zygosaccharomyces bailii ISA 1307 was constructed in pRS316, a shuttle vector for Saccharomyces cerevisiae and Escherichia coli. The library has an average insert size of 6 kb and covers the genome more than 20 times assuming a genome size similar to that of S. cerevisiae. This new tool has been successfully used, by us and others, to isolate Z. bailii genes. One example is the beta-isopropylmalate dehydrogenase gene (ZbLEU2) of Z. bailii, which was cloned by complementation of a leu2 mutation in S. cerevisiae. An open reading frame encoding a protein with a molecular mass of 38.7 kDa was found. The nucleotide sequence of ZbLEU2 and the deduced amino acid sequence showed a significant degree of identity to those of beta-isopropylmalate dehydrogenases from several other yeast species. The sequence of ZbLEU2 has been deposited in the EMBL data library under accession number AJ292544.

  15. 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

  16. Analysis of dormant bud (Banjhi) specific transcriptome of tea (Camellia sinensis (L.) O. Kuntze) from cDNA library revealed dormancy-related genes.

    PubMed

    Thirugnanasambantham, Krishnaraj; Prabu, Gajjeraman; Palanisamy, Senthilkumar; Chandrabose, Suresh Ramraj Subhas; Mandal, Abul Kalam Azad

    2013-02-01

    Bud dormancy is of ecological and economical interest due to its impact on tea (Camellia sinensis (L.) O. Kuntze) plant growth and yield. Growth regulation associated with dormancy is an essential element in plant's life cycle that leads to changes in expression of large number of genes. In order to identify and provide a picture of the transcriptome profile, cDNA library was constructed from dormant bud (banjhi) of tea. Sequence and gene ontology analysis of 3,500 clones, in many cases, enabled their functional categorization concerning the bud growth. Based on the cDNA library data, the putative role of identified genes from tea is discussed in relation to growth and dormancy, which includes morphogenesis, cellular differentiation, tropism, cell cycle, signaling, and various metabolic pathways. There was a higher representation of unknown processes such as unknown molecular functions (65.80 %), unknown biological processes (62.46 %), and unknown cellular components (67.42 %). However, these unknown transcripts represented a novel component of transcripts in tea plant bud growth and/or dormancy development. The identified transcripts and expressed sequence tags provides a valuable public resource and preliminary insights into the molecular mechanisms of bud dormancy regulation. Further, the findings will be the target of future expression experiments, particularly for further identification of dormancy-related genes in this species.

  17. Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies

    PubMed Central

    Bacchetti De Gregoris, Tristano; Borra, Marco; Biffali, Elio; Bekel, Thomas; Burgess, J Grant; Kirby, Richard R; Clare, Anthony S

    2009-01-01

    Background Balanus amphitrite is a barnacle commonly used in biofouling research. Although many aspects of its biology have been elucidated, the lack of genetic information is impeding a molecular understanding of its life cycle. As part of a wider multidisciplinary approach to reveal the biogenic cues influencing barnacle settlement and metamorphosis, we have sequenced and annotated the first cDNA library for B. amphitrite. We also present a systematic validation of potential reference genes for normalization of quantitative real-time PCR (qRT-PCR) data obtained from different developmental stages of this animal. Results We generated a cDNA library containing expressed sequence tags (ESTs) from adult B. amphitrite. A total of 609 unique sequences (comprising 79 assembled clusters and 530 singlets) were derived from 905 reliable unidirectionally sequenced ESTs. Bioinformatics tools such as BLAST, HMMer and InterPro were employed to allow functional annotation of the ESTs. Based on these analyses, we selected 11 genes to study their ability to normalize qRT-PCR data. Total RNA extracted from 7 developmental stages was reverse transcribed and the expression stability of the selected genes was compared using geNorm, BestKeeper and NormFinder. These software programs produced highly comparable results, with the most stable gene being mt-cyb, while tuba, tubb and cp1 were clearly unsuitable for data normalization. Conclusion The collection of B. amphitrite ESTs and their annotation has been made publically available representing an important resource for both basic and applied research on this species. We developed a qRT-PCR assay to determine the most reliable reference genes. Transcripts encoding cytochrome b and NADH dehydrogenase subunit 1 were expressed most stably, although other genes also performed well and could prove useful to normalize gene expression studies. PMID:19552808

  18. Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis.

    PubMed

    Kanjanawattanawong, Supanath; Tangphatsornruang, Sithichoke; Triwitayakorn, Kanokporn; Ruang-areerate, Panthita; Sangsrakru, Duangjai; Poopear, Supannee; Somyong, Suthasinee; Narangajavana, Jarunya

    2014-10-01

    The para rubber tree is the most widely cultivated tree species for producing natural rubber (NR) latex. Unfortunately, rubber tree characteristics such as a long life cycle, heterozygous genetic backgrounds, and poorly understood genetic profiles are the obstacles to breeding new rubber tree varieties, such as those with improved NR yields. Recent evidence has revealed the potential importance of controlling microRNA (miRNA) decay in some aspects of NR regulation. To gain a better understanding of miRNAs and their relationship with rubber tree gene regulation networks, large genomic DNA insert-containing libraries were generated to complement the incomplete draft genome sequence and applied as a new powerful tool to predict a function of interested genes. Bacterial artificial chromosome and fosmid libraries, containing a total of 120,576 clones with an average insert size of 43.35 kb, provided approximately 2.42 haploid genome equivalents of coverage based on the estimated 2.15 gb rubber tree genome. Based on these library sequences, the precursors of 1 member of rubber tree-specific miRNAs and 12 members of conserved miRNAs were successfully identified. A panel of miRNAs was characterized for phytohormone response by precisely identifying phytohormone-responsive motifs in their promoter sequences. Furthermore, the quantitative real-time PCR on ethylene stimulation of rubber trees was performed to demonstrate that the miR2118, miR159, miR164 and miR166 are responsive to ethylene, thus confirmed the prediction by genomic DNA analysis. The cis-regulatory elements identified in the promoter regions of these miRNA genes help augment our understanding of miRNA gene regulation and provide a foundation for further investigation of the regulation of rubber tree miRNAs.

  19. Construction of cDNA library from intestine, mesentery and coelomocyte of Apostichopus japonicus Selenka infected with Vibrio sp. and a preliminary analysis of immunity-related genes

    NASA Astrophysics Data System (ADS)

    Liu, Hongzhan; Zheng, Fengrong; Sun, Xiuqin; Cai, Yimei

    2012-06-01

    The aquaculture of sea cucumber Apostichopus japonicus (Echinodermata, Holothuroidea) has grown rapidly during recent years and has become an important sector of the marine industry in Northern China. However, with the rapid growth of the industry and the use of non-standard culture techniques, epidemic diseases of A. japonicus now pose increasing problems to the industry. To screen the genes with stress response to bacterial infection in sea cucumber at a genome wide level, we constructed a cDNA library from A. japonicus Selenka (Aspidochirotida: Stichopodidae) after infecting them with Vibrio sp. for 48 h. Total RNA was extracted from the intestine, mesentery and coelomocyte of infected sea cucumber using Trizol and mRNA was isolated by Oligotex mRNA Kits. The ligated cDNAs were transformed into DH5α, and a library of 3.24×105 clones (3.24×105 cfu mL-1) was obtained with the sizes of inserted fragments ranging from 0.8 to 2.5 kb. Sequencing the cDNA clones resulted in a total of 1106 ESTs that passed the quality control. BlastX and BlastN searches have identified 168 (31.5%) ESTs sharing significant homology with known sequences in NCBI protein or nucleotide databases. Among a panel of 25 putative immunity-related genes, serum lectin isoform, complement component 3, complement component 3-like genes were further studied by real-time PCR and they all increased more than 5 fold in response to Vibrio sp. challenge. Our library provides a valuable molecular tool for future study of invertebrate immunity against bacterial infection and our gene expression data indicates the importance of the immune system in the evolution and development of sea cucumber.

  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. Library Computing.

    ERIC Educational Resources Information Center

    Dayall, Susan A.; And Others

    1987-01-01

    Six articles on computers in libraries discuss training librarians and staff to use new software; appropriate technology; system upgrades of the Research Libraries Group's information system; pre-IBM PC microcomputers; multiuser systems for small to medium-sized libraries; and a library user's view of the traditional card catalog. (EM)

  2. Library Buildings.

    ERIC Educational Resources Information Center

    Manley, Will; And Others

    1989-01-01

    The innovative designs of three libraries are described: the Tempe (Arizona) Public Library, which emphasizes services for children and students; an underground library at Park College, Missouri; and a public library located in the Vancouver (Washington) Mall. The fourth article describes the work going on to restore the Los Angeles (California)…

  3. A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

    PubMed Central

    Marques, M Carmen; Alonso-Cantabrana, Hugo; Forment, Javier; Arribas, Raquel; Alamar, Santiago; Conejero, Vicente; Perez-Amador, Miguel A

    2009-01-01

    Background Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation. Results We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis. Conclusion The new EST collection denotes an

  4. Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction.

    PubMed

    Malone, Marie L; Cavett, Valerie J; Paegel, Brian M

    2017-01-09

    Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼10(6) primers/2.8-μm-diameter bead) via either azide-alkyne click chemistry or Michael addition. The primers are viable polymerase substrates (4-7% bead-immobilized enzymatic extension product yield from one thermal cycle). Carbodiimide-activated carboxylic acid beads only react with oligonucleotides under conditions that promote nonspecific interactions (low salt, low pH, no detergent), comparably immobilizing primers on beads, but yielding no detectable enzymatic extension product. Click-functionalized beads perform satisfactorily in emPCR of a site-saturation mutagenesis library, generating monoclonal templated beads (10(4)-10(5) copies/bead, 1.4-kb amplicons). This simpler, chemical approach to primer immobilization may spur more economical library preparation for high-throughput sequencing and enable more complex surface elaboration for in vitro evolution.

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

    PubMed Central

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

    2016-01-01

    Motivation: CRISPR-derived RNA guided endonucleases (RGENs) have been widely used for both gene knockout and knock-in at the level of single or multiple genes. RGENs are now available for forward genetic screens at genome scale, but single guide RNA (sgRNA) selection at this scale is difficult. Results: We develop an online tool, Cas-Database, a genome-wide gRNA library design tool for Cas9 nucleases from Streptococcus pyogenes (SpCas9). With an easy-to-use web interface, Cas-Database allows users to select optimal target sequences simply by changing the filtering conditions. Furthermore, it provides a powerful way to select multiple optimal target sequences from thousands of genes at once for the creation of a genome-wide library. Cas-Database also provides a web application programming interface (web API) for advanced bioinformatics users. Availability and implementation: Free access at http://www.rgenome.net/cas-database/. Contact: sangsubae@hanyang.ac.kr or jskim01@snu.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153724

  6. Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing▿ †

    PubMed Central

    Sagaram, Uma Shankar; DeAngelis, Kristen M.; Trivedi, Pankaj; Andersen, Gary L.; Lu, Shi-En; Wang, Nian

    2009-01-01

    The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. “Candidatus Liberibacter asiaticus” was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of “Candidatus Liberibacter asiaticus” in symptomatic leaves. These data implicate “Candidatus Liberibacter asiaticus” as the pathogen responsible for HLB disease. PMID:19151177

  7. [Dominant phylotypes in the 16S rRNA gene clone libraries from bacterial mats of the Uzon caldera (Kamchatka, Russia) hydrothermal springs].

    PubMed

    Akimov, V N; Podosokorskaia, O A; Shliapnikov, M G; Gal'chenko, V F

    2013-01-01

    In situ analysis of the 16S rRNA genes form bacterial mats of five hydrothermal springs (36-58 degrees C) in the Uzon caldera (Kamchatka, Russia) was carried out using clone libraries. Eight clone libraries contained 18 dominant phylotypes (over 4-5%). In most clone libraries, the phylotype of the green sulfur bacterium Chlorobaculum sp. was among the dominant ones. The phylotypes of the green nonsulfur bacteria Chloroflexus and Roseiflexus and of purple nonsulfur bacteria Rhodoblastus, Rhodopseudomonas, and Rhodoferax were also among the dominant ones. Cyanobacteria were represented by one dominant phylotype in a single spring. Among nonphototrophic bacteria, the dominant phylotypes belonged to Sulfyrihydrogenibium sp., Geothrixsp., Acidobacterium sp., Meiothermus sp., Thiomonas sp., Thiofaba sp., and Spirochaeta sp. Three phylotypes were not identified at the genus level. Most genera of phototrophic and nonphototrophic organisms corresponding to the phylotypes from Uzon hydrotherms have been previously revealed in the hydrotherms of volcanically active regions of America, Asia, and Europe. These results indicate predominance of bacterial mats carrying out anaerobic photosynthesis in the hydrotherms of the Uzon caldera.

  8. Effects of the EVCAM chemical validation library on differentiation using marker gene expression in lmouse embryonic stem cells

    EPA Science Inventory

    The adherent cell differentiation and cytotoxicity (ACDC) assay was used to profile the effects of the ECVAM EST validation chemical library (19 compounds) on J1 mouse embryonic stem cells (mESC). PCR-based TaqMan Low Density Arrays (TLDA) provided a high-content assessment of al...

  9. 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)

  10. Isolation of SMA candidate genes from a YAC contig by direct selection of cDNA clones from normalized cDNA libraries

    SciTech Connect

    Ross, B.M.; Bonaldo, M.F.; Vitale, E.

    1994-09-01

    A YAC contig has been constructed across the spinal muscular atrophy (SMA) region of chromosome 5 (5q11-13). Further definition by pedigree analysis has yielded a minimal genetic region of 400 kb. For isolation of candidate genes in this region, the following cDNA selection method was hybridized to directionally cloned normalized (Cot 1 DNA-preannealed) cDNA libraries in the form of single-stranded circles. The libraries used were constructed from SMA infant brain and normal fetal liver+spleen. Hybridizing circles were eluted off the filter, partially converted into duplexes and electroporated into bacteria. The selected clones were then sequentially hybridized with a human Cot 1 DNA probe (BRL), and a probe made from the corresponding YAC DNA. Clones that hybridized only to the YAC DNA probe were verified to map to the critical region by genomic Southern analyses. Ten different cDNA clones have been isolated by this procedure so far. Three of them have been definitively mapped back to the region. Four of the ten clones are now completely sequenced. One clone shows sequence homology to a transcriptional initiation factor; another has homology to a prokaryotic attachment site sequence for the lipid moiety of membrane lipoproteins. Two clones show no homology to sequences represented in the public databases. We are continuing the full characterization of the cDNA clones as candidates for the SMA gene.

  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. Identification of low Ca(2+) stress-induced embryo apoptosis response genes in Arachis hypogaea by SSH-associated library lift (SSHaLL).

    PubMed

    Chen, Hua; Zhang, Chong; Cai, Tie Cheng; Deng, Ye; Zhou, Shuangbiao; Zheng, Yixiong; Ma, Shiwei; Tang, Ronghua; Varshney, Rajeev K; Zhuang, Weijian

    2016-02-01

    Calcium is a universal signal in the regulation of wide aspects in biology, but few are known about the function of calcium in the control of early embryo development. Ca(2+) deficiency in soil induces early embryo abortion in peanut, producing empty pods, which is a general problem; however, the underlying mechanism remains unclear. In this study, embryo abortion was characterized to be caused by apoptosis marked with cell wall degradation. Using a method of SSH cDNA libraries associated with library lift (SSHaLL), 62 differentially expressed genes were isolated from young peanut embryos. These genes were classified to be stress responses, catabolic process, carbohydrate and lipid metabolism, embryo morphogenesis, regulation, etc. The cell retardation with cell wall degradation was caused by up-regulated cell wall hydrolases and down-regulated cellular synthases genes. HsfA4a, which was characterized to be important to embryo development, was significantly down-regulated under Ca(2+) -deficient conditions from 15 days after pegging (DAP) to 30 DAP. Two AhCYP707A4 genes, encoding abscisic acid (ABA) 8'-hydroxylases, key enzymes for ABA catabolism, were up-regulated by 21-fold under Ca(2+) -deficient conditions upstream of HsfA4a, reducing the ABA level in early embryos. Over-expression of AhCYP707A4 in Nicotiana benthamiana showed a phenotype of low ABA content with high numbers of aborted embryos, small pods and less seeds, which confirms that AhCYP707A4 is a key player in regulation of Ca(2+) deficiency-induced embryo abortion via ABA-mediated apoptosis. The results elucidated the mechanism of low Ca(2+) -induced embryo abortion and described the method for other fields of study.

  13. Detection of Genes Modifying Sensitivity to Proteasome Inhibitors Using a shRNA Library in Breast Cancer

    DTIC Science & Technology

    2008-03-01

    backbone of the primary miR-30 microRNA14. We have produced and sequence -verified more than 200,000 shRNAs covering almost all of the predicted...the complement of these sequences . One can assess cellular response to different treatments 5 by comparing barcode representations of cell...Barcode sequences were determined for the human shRNA library, and custom, multiplex format microarrays were prepared that contained both barcode

  14. Use of antibody gene library for the isolation of specific single chain antibodies by ampicillin-antigen conjugates.

    PubMed

    Neumann-Schaal, Meina; Messerschmidt, Katrin; Grenz, Nicole; Heilmann, Katja

    2013-03-01

    Isolation of recombinant antibodies from antibody libraries is commonly performed by different molecular display formats including phage display and ribosome display or different cell-surface display formats. We describe a new method which allows the selection of Escherichia coli cells producing the required single chain antibody by cultivation in presence of ampicillin conjugated to the antigen of interest. The method utilizes the neutralization of the conjugate by the produced single chain antibody which is secreted to the periplasm. Therefore, a new expression system based on the pET26b vector was designed and a library was constructed. The method was successfully established first for the selection of E. coli BL21 Star (DE3) cells expressing a model single chain antibody (anti-fluorescein) by a simple selection assay on LB-agar plates. Using this selection assay, we could identify a new single chain antibody binding biotin by growing E. coli BL21 Star (DE3) containing the library in presence of a biotin-ampicillin conjugate. In contrast to methods as molecular or cell surface display our selection system applies the soluble single chain antibody molecule and thereby avoids undesired effects, e.g. by the phage particle or the yeast fusion protein. By selecting directly in an expression strain, production and characterization of the selected single chain antibody is possible without any further cloning or transformation steps.

  15. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches.

    PubMed

    Lorieux, Mathias; Blein, Mélisande; Lozano, Jaime; Bouniol, Mathieu; Droc, Gaétan; Diévart, Anne; Périn, Christophe; Mieulet, Delphine; Lanau, Nadège; Bès, Martine; Rouvière, Claire; Gay, Céline; Piffanelli, Pietro; Larmande, Pierre; Michel, Corinne; Barnola, Isabelle; Biderre-Petit, Corinne; Sallaud, Christophe; Perez, Pascual; Bourgis, Fabienne; Ghesquière, Alain; Gantet, Pascal; Tohme, Joe; Morel, Jean Benoit; Guiderdoni, Emmanuel

    2012-06-01

    We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions.

  16. Isolation of novel and known genes from a human fetal cochlear cDNA library using subtractive hybridization and differential screening

    SciTech Connect

    Robertson, N.G.; Gutierrez-Espeleta, G.A.; Bieber, F.R. |

    1994-09-01

    We used a combination of subtractive hybridization and differential screening strategies to identify genes that may function normally in hearing and, when mutated, result in deafness. A human fetal cochlear (membranous labyrinth) cDNA library was subtracted against total human fetal brain RNAs by an avidin-biotin-based procedure to enrich for cochlear transcripts. Subtracted cochlear clones were differentially screened with {sup 32}P-labeled total cochlear and total brain cDNA probes. Sequence analysis of clones that hybridized more intensely with cochlear than with brain cDNA probes revealed some previously characterized genes, including mitochondrial sequences, collagen type I {alpha}-2 (COL1A2), collagen type II {alpha}-1 (COL2A1), collagen type III {alpha}-1 (COL3A1), spermidine/spermine N{sup 1}-acetyltransferase (SAT), osteonectin (SPARC), and peripheral myelin protein 22 (PMP22). Also identified were clones that are potential novel cochlear genes. Northern blots of cochlear and brain RNAs probed with COL1A2, COL2A1, COL3A1, SAT, SPARC, PMP22, and a novel sequence, designated Coch-5B2, confirm results of the subtractive procedure by showing preferential cochlear expression. A number of these genes serve structural or regulatory functions in extracellular matrix or neural conduction; defects in some of these genes are associated with disorders involving hearing loss. Partial sequence analysis of Coch-5B2 reveals a von Willebrand factor type A-like domain in this cDNA. To assess the cochlear specificity of Coch-5B2, a Northern blot panel of 14 human fetal tissue RNAs was probed with Coch-5B2, showing differential expression of this novel gene in the cochlea. 68 refs., 3 figs.

  17. Base Composition-Independent Hybridization in Tetramethylammonium Chloride: A Method for Oligonucleotide Screening of Highly Complex Gene Libraries

    NASA Astrophysics Data System (ADS)

    Wood, William I.; Gitschier, Jane; Lasky, Laurence A.; Lawn, Richard M.

    1985-03-01

    An oligonucleotide hybridization procedure has been developed that eliminates the preferential melting of A\\cdot T versus G\\cdot C base pairs, allowing the stringency of the hybridization to be controlled as a function of probe length only. This technique, which uses tetramethylammonium chloride, is especially helpful whenever a highly complex library is screened with a pool of oligonucleotide probes, which usually vary widely in base composition. The procedure can also be applied advantageously whenever an exact match to an oligonucleotide probe is desired, such as in screening for clones having as little as a single-base alteration generated by in vitro mutagenesis.

  18. Seasonal Diversity of Planktonic Protists in Southwestern Alberta Rivers over a 1-Year Period as Revealed by Terminal Restriction Fragment Length Polymorphism and 18S rRNA Gene Library Analyses

    PubMed Central

    Thomas, Matthew C.; Selinger, L. Brent

    2012-01-01

    The temporal dynamics of planktonic protists in river water have received limited attention despite their ecological significance and recent studies linking phagotrophic protists to the persistence of human-pathogenic bacteria. Using molecular-based techniques targeting the 18S rRNA gene, we studied the seasonal diversity of planktonic protists in Southwestern Alberta rivers (Oldman River Basin) over a 1-year period. Nonmetric multidimensional scaling analysis of terminal restriction fragment length polymorphism (T-RFLP) data revealed distinct shifts in protistan community profiles that corresponded to season rather than geographical location. Community structures were examined by using clone library analysis; HaeIII restriction profiles of 18S rRNA gene amplicons were used to remove prevalent solanaceous plant clones prior to sequencing. Sanger sequencing of the V1-to-V3 region of the 18S rRNA gene libraries from spring, summer, fall, and winter supported the T-RFLP results and showed marked seasonal differences in the protistan community structure. The spring library was dominated by Chloroplastidae (29.8%), Centrohelida (28.1%), and Alveolata (25.5%), while the summer and fall libraries contained primarily fungal clones (83.0% and 88.0%, respectively). Alveolata (35.6%), Euglenozoa (24.4%), Chloroplastida (15.6%), and Fungi (15.6%) dominated the winter library. These data demonstrate that planktonic protists, including protozoa, are abundant in river water in Southwestern Alberta and that conspicuous seasonal shifts occur in the community structure. PMID:22685143

  19. 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.

  20. Detection of Genes Modifying Sensitivity to Proteasome Inhibitors Using a shRNA Library in Breast Cancer

    DTIC Science & Technology

    2009-03-01

    and sequence -verified more than 200,000 shRNAs covering almost all of the predicted genes in the mouse and human genomes15 and have used these...The Human DiGeorge Syndrome Critical Region Gene 8 8 and Its D. melanogaster Homolog Are Required for miRNA Biogenesis. Curr Biol 14, 2162

  1. 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,…

  2. Construction and analysis of the cDNA subtraction library of yeast and mycelial phases of Sporothrix globosa isolated in China: identification of differentially expressed genes*

    PubMed Central

    Hu, Qing-bi; He, Yu; Zhou, Xun

    2015-01-01

    Species included in the Sporothrix schenckii complex are temperature-dependent with dimorphic growth and cause sporotrichosis that is characterized by chronic and fatal lymphocutaneous lesions. The putative species included in the Sporothrix complex are S. brasiliensis, S. globosa, S. mexicana, S. pallida, S. schenckii, and S. lurei. S. globosa is the causal agent of sporotrichosis in China, and its pathogenicity appears to be closely related to the dimorphic transition, i.e. from the mycelial to the yeast phase, it adapts to changing environmental conditions. To determine the molecular mechanisms of the switching process that mediates the dimorphic transition of S. globosa, suppression subtractive hybridization (SSH) was used to prepare a complementary DNA (cDNA) subtraction library from the yeast and mycelial phases. Bioinformatics analysis was performed to profile the relationship between differently expressed genes and the dimorphic transition. Two genes that were expressed at higher levels by the yeast form were selected, and their differential expression levels were verified using a quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR). It is believed that these differently expressed genes are involved in the pathogenesis of S. globosa infection in China. PMID:26642182

  3. Identification and characterization of a novel thermostable gh-57 gene from metagenomic fosmid library of the Juan de Fuca Ridge hydrothemal vent.

    PubMed

    Wang, Hui; Gong, Yingxue; Xie, Wei; Xiao, Wenjuan; Wang, Junmei; Zheng, Yangyang; Hu, Jia; Liu, Zehuan

    2011-08-01

    A novel glycoside hydrolases family 57 gene (gh-57) was found from a metagenomic fosmid library constructed from a black smoker chimney sample 4143-1 from the Mothra hydrothermal vent at the Juan de Fuca Ridge. Sequence and homology analysis using BLAST revealed that it had high similarity to gh-57 family. Conserved domain research revealed that the novel gh-57 contained a Glyco-hydro-57 domain and five conserved regions, including two putative catalytic residues Glu¹⁵⁴ and Asp²⁶³. The three-dimensional features of the protein and its homologue from Pyrococcus horikoshii OT3 known as α-amylase were generated by homology modeling. The gh-57 gene was cloned, expressed, and purified in Escherichia coli using pQE system. Enzyme activity revealed that the recombinant protein could hydrolyze soluble starch and demonstrated amylase activity. It showed an optimal pH of 7.5, an optimal temperature of 90 °C, and its thermostability at 90 °C could remain over 50% enzyme activity for 4 h. The enzyme activity could be increased by DTT and Mg²⁺ while an inhibitory effect was observed with EDTA, ATP, and Ca²⁺. These results showed that the gh-57 gene was a novel thermostable amylase from oceanic microorganisms.

  4. Construction and analysis of an SSH cDNA library of early heat-induced genes of Vigna aconitifolia variety RMO-40.

    PubMed

    Rampuria, Sakshi; Joshi, Uma; Palit, Paramita; Deokar, Amit A; Meghwal, Raju R; Mohapatra, T; Srinivasan, R; Bhatt, K V; Sharma, Ramavtar

    2012-11-01

    Moth bean ( Vigna aconitifolia (Jacq.) Marechal) is an important grain legume crop grown in rain fed areas of hot desert regions of Thar, India, under scorching sun rays with very little supplementation of water. An SSH cDNA library was generated from leaf tissues of V. aconitifolia var. RMO-40 exposed to an elevated temperature of 42 °C for 5 min to identify early-induced genes. A total of 488 unigenes (114 contigs and 374 singletons) were derived by cluster assembly and sequence alignment of 738 ESTs; out of 206 ESTs (28%) of unknown proteins, 160 ESTs (14%) were found to be novel to moth bean. Only 578 ESTs (78%) showed significant BLASTX similarity (<1 × 10(-6)) in the NCBI non-redundant database. Gene ontology functional classification terms were retrieved for 479 (65%) sequences, and 339 sequences were annotated with 165 EC codes and mapped to 68 different KEGG pathways. Four hundred and fifty-two ESTs were further annotated with InterProScan (IPS), and no IPS was assigned to 153 ESTs. In addition, the expression level of 27 ESTs in response to heat stress was evaluated through semiquantitative RT-PCR assay. Approximately 20 different signaling genes and 16 different transcription factors have been shown to be associated with heat stress in moth bean for the first time.

  5. Depth matters: Microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries

    NASA Astrophysics Data System (ADS)

    Schnetzer, Astrid; Moorthi, Stefanie D.; Countway, Peter D.; Gast, Rebecca J.; Gilg, Ilana C.; Caron, David A.

    2011-01-01

    Protistan community structure was examined from 6 depths (1.5, 20, 42, 150, 500, 880 m) at a coastal ocean site in the San Pedro Channel, California. A total of 856 partial length 18S rDNA protistan sequences from the six clone libraries were analyzed to characterize diversity present at each depth. The sequences were grouped into a total of 259 Operational Taxonomic Units (OTUs) that were inferred using an automated OTU calling program that formed OTUs with approximately species-level distinction (95% sequence similarity). Most OTUs (194 out of 259) were observed at only one specific depth, and only two were present in clone libraries from all depths. OTUs were obtained from 21 major protistan taxonomic groups determined by their closest BLAST matches to identified protists in the NCBI database. Approximately 74% of the detected OTUs belonged to the Chromalveolates, with Group II alveolates making up the largest single group. Protistan assemblages at euphotic depths (1.5, 20 and 42 m) were characterized by the presence of clades that contained phototrophic species (stramenopiles, chlorophytes and haptophytes) as well as consumers (especially ciliates). Assemblages in the lower water column (150, 500 and 800 m) were distinct from communities at shallow depths because of strong contributions from taxa belonging to euglenozoans, acantharians, polycystines and Taxopodida ( Sticholonche spp. and close relatives). Species richness (Chao I estimate) and diversity (Shannon index) were highest within the euphotic zone and at 150 m, and lowest for protistan assemblages located in the oxygen minimum zone (500 and 880 m). Multivariate analyses (Bray-Curtis coefficient) confirmed that protistan assemblage composition differed significantly when samples were grouped into shallow (≤150 m) and deep water assemblages (≥150 m).

  6. A novel esterase gene cloned from a metagenomic library from neritic sediments of the South China Sea

    PubMed Central

    2011-01-01

    Background Marine microbes are a large and diverse group, which are exposed to a wide variety of pressure, temperature, salinity, nutrient availability and other environmental conditions. They provide a huge potential source of novel enzymes with unique properties that may be useful in industry and biotechnology. To explore the lipolytic genetic resources in the South China Sea, 23 sediment samples were collected in the depth < 100 m marine areas. Results A metagenomic library of South China Sea sediments assemblage in plasmid vector containing about 194 Mb of community DNA was prepared. Screening of a part of the unamplified library resulted in isolation of 15 unique lipolytic clones with the ability to hydrolyze tributyrin. A positive recombinant clone (pNLE1), containing a novel esterase (Est_p1), was successfully expressed in E. coli and purified. In a series of assays, Est_p1 displayed maximal activity at pH 8.57, 40°C, with ρ-Nitrophenyl butyrate (C4) as substrate. Compared to other metagenomic esterases, Est_p1 played a notable role in specificity for substrate C4 (kcat/Km value 11,500 S-1m M-1) and showed no inhibited by phenylmethylsulfonyl fluoride, suggested that the substrate binding pocket was suitable for substrate C4 and the serine active-site residue was buried at the bottom of substrate binding pocket which sheltered by a lid structure. Conclusions Esterase, which specificity towards short chain fatty acids, especially butanoic acid, is commercially available as potent flavoring tools. According the outstanding activity and specificity for substrate C4, Est_p1 has potential application in flavor industries requiring hydrolysis of short chain esters. PMID:22067554

  7. 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…

  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…

  9. 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…

  10. Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries.

    PubMed

    Lorenz, W Walter; Sun, Feng; Liang, Chun; Kolychev, Dmitri; Wang, Haiming; Zhao, Xin; Cordonnier-Pratt, Marie-Michele; Pratt, Lee H; Dean, Jeffrey F D

    2006-01-01

    Drought stress is the principal cause of seedling mortality in pine forests of the southeastern United States and in many other forested regions around the globe. As part of a larger effort to discover loblolly pine genes, this study subjected rooted cuttings of three unrelated pine genotypes to three watering regimens. Expressed sequence tags (ESTs) were obtained from both the 3' and 5' ends of 12,918 randomly selected cDNAs generated from root tissues. These ESTs were clustered to identify 6,765 unique transcripts (UniScripts) derived from 6,202 putative unique genes (UniGenes-S). Tentative annotations were assigned on the basis of BLASTX comparisons to the Protein Information Resource Nonredundant Reference (PIR-NREF) database. Expression levels of 42 UniScripts varied with high statistical significance with respect to treatment. Many of them resembled gene products shown to be important for drought tolerance in other species, including dehydrins, endochitinases, cytochrome P450 enzymes, pathogenesis-related proteins and various late-embryogenesis abundant (LEA) gene products. Similarly, expression levels of 110 UniScripts varied with high statistical significance among genotypes, indicating that gene expression patterns in this species are much more dependent on genotype than on treatment. Most of the water stress-induced pine UniScripts that appeared to encode products resembling drought tolerance factors in other species were most highly induced in a single genotype, suggesting that particularly useful adaptive alleles for drought tolerance might exist within the collection of cDNAs characterized from this genotype. Mining and visualizing the complete data set, as well as downloading of both EST and UniScript contig sequences, are possible using MAGIC Gene Discovery at http://fungen.org/genediscovery/.

  11. An internal ribosome entry site (IRES) mutant library for tuning expression level of multiple genes in mammalian cells.

    PubMed

    Koh, Esther Y C; Ho, Steven C L; Mariati; Song, Zhiwei; Bi, Xuezhi; Bardor, Muriel; Yang, Yuansheng

    2013-01-01

    A set of mutated Encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) elements with varying strengths is generated by mutating the translation initiation codons of 10(th), 11(th), and 12(th) AUG to non-AUG triplets. They are able to control the relative expression of multiple genes over a wide range in mammalian cells in both transient and stable transfections. The relative strength of each IRES mutant remains similar in different mammalian cell lines and is not gene specific. The expressed proteins have correct molecular weights. Optimization of light chain over heavy chain expression by these IRES mutants enhances monoclonal antibody expression level and quality in stable transfections. Uses of this set of IRES mutants can be extended to other applications such as synthetic biology, investigating interactions between proteins and its complexes, cell engineering, multi-subunit protein production, gene therapy, and reprogramming of somatic cells into stem cells.

  12. An Epigenetic Compound Library Screen Identifies BET Inhibitors That Promote HSV-1 and -2 Replication by Bridging P-TEFb to Viral Gene Promoters through BRD4.

    PubMed

    Ren, Ke; Zhang, Wei; Chen, Xiaoqing; Ma, Yingyu; Dai, Yue; Fan, Yimei; Hou, Yayi; Tan, Ren Xiang; Li, Erguang

    2016-10-01

    The human HSV-1 and -2 are common pathogens of human diseases. Both host and viral factors are involved in HSV lytic infection, although detailed mechanisms remain elusive. By screening a chemical library of epigenetic regulation, we identified bromodomain-containing protein 4 (BRD4) as a critical player in HSV infection. We show that treatment with pan BD domain inhibitor enhanced both HSV infection. Using JQ1 as a probe, we found that JQ1, a defined BD1 inhibitor, acts through BRD4 protein since knockdown of BRD4 expression ablated JQ1 effect on HSV infection. BRD4 regulates HSV replication through complex formation involving CDK9 and RNAP II; whereas, JQ1 promotes HSV-1 infection by allocating the complex to HSV gene promoters. Therefore, suppression of BRD4 expression or inhibition of CDK9 activity impeded HSV infection. Our data support a model that JQ1 enhances HSV infection by switching BRD4 to transcription regulation of viral gene expression from chromatin targeting since transient expression of BRD4 BD1 or BD1/2 domain had similar effect to that by JQ1 treatment. In addition to the identification that BRD4 is a modulator for JQ1 action on HSV infection, this study demonstrates BRD4 has an essential role in HSV infection.

  13. An Epigenetic Compound Library Screen Identifies BET Inhibitors That Promote HSV-1 and -2 Replication by Bridging P-TEFb to Viral Gene Promoters through BRD4

    PubMed Central

    Chen, Xiaoqing; Ma, Yingyu; Dai, Yue; Fan, Yimei; Hou, Yayi; Tan, Ren Xiang

    2016-01-01

    The human HSV-1 and -2 are common pathogens of human diseases. Both host and viral factors are involved in HSV lytic infection, although detailed mechanisms remain elusive. By screening a chemical library of epigenetic regulation, we identified bromodomain-containing protein 4 (BRD4) as a critical player in HSV infection. We show that treatment with pan BD domain inhibitor enhanced both HSV infection. Using JQ1 as a probe, we found that JQ1, a defined BD1 inhibitor, acts through BRD4 protein since knockdown of BRD4 expression ablated JQ1 effect on HSV infection. BRD4 regulates HSV replication through complex formation involving CDK9 and RNAP II; whereas, JQ1 promotes HSV-1 infection by allocating the complex to HSV gene promoters. Therefore, suppression of BRD4 expression or inhibition of CDK9 activity impeded HSV infection. Our data support a model that JQ1 enhances HSV infection by switching BRD4 to transcription regulation of viral gene expression from chromatin targeting since transient expression of BRD4 BD1 or BD1/2 domain had similar effect to that by JQ1 treatment. In addition to the identification that BRD4 is a modulator for JQ1 action on HSV infection, this study demonstrates BRD4 has an essential role in HSV infection. PMID:27764245

  14. Sequence analysis of expressed sequence tags from an ABA-treated cDNA library identifies stress response genes in the moss Physcomitrella patens.

    PubMed

    Machuka, J; Bashiardes, S; Ruben, E; Spooner, K; Cuming, A; Knight, C; Cove, D

    1999-04-01

    Partial cDNA sequencing was used to obtain 169 expressed sequence tags (ESTs) in the moss, Physcomitrella patens. The source of ESTs was a random cDNA library constructed from 7 day-old protonemata following treatment with 10(-4) M abscisic acid (ABA). Analysis of the ESTs identified 69% with homology to known sequences, 61% of which had significant homology to sequences of plant origin. More importantly, at least 11 ESTs had significant similarities to genes which are implicated in plant stress-responses, including responses which may involve ABA. These included a cDNA associated with desiccation tolerance, two heat shock protein genes, one cold acclimation protein cDNA and five others that may be involved in either oxidative or chemical stress or both, i.e., Zn/Cu-superoxide dismutase, NADPH protochlorophyllide oxidoreductase (PorB), selenium binding protein, glutathione peroxidase and glutathione S transferase. Analysis of codon usage between P. patens and seed plants indicated that although mosses and higher plants are to a large extent similar, minor variations also exists that may represent the distinctiveness of each group.

  15. Characterization of MMP-9 gene from a normalized cDNA library of kidney tissue of yellow catfish (Pelteobagrus fulvidraco).

    PubMed

    Ke, Fei; Wang, Yun; Hong, Jun; Xu, Chen; Chen, Huan; Zhou, Shuai-Bang

    2015-08-01

    Matrix metalloproteinase-9 (MMP-9), one of members of the MMP family, is important for the cleaving of structural extracellular matrix (ECM) molecules and involved in inflammatory processes. In this study, MMP-9 cDNA was isolated and characterized from a normalized cDNA library of kidney tissue of yellow catfish (designated as YcMMP-9). The complete sequence of YcMMP-9 cDNA consisted of 2561 nucleotides. The open reading frame potentially encoded a protein of 685 amino acids with a calculated molecular mass of approximately 77.182 kDa. Amino acid sequence of YcMMP-9 have typical characteristics of MMP-9 family and showed highest identity (85.3%) to channel catfish MMP-9. The YcMMP-9 genomic DNA contains 13 exons and 12 introns. Quantitative RT-PCR (qRT-PCR) analysis showed that YcMMP-9 mRNA was constitutively expressed in all examined tissues in normal fish with high expression in head kidney, trunk kidney, blood, and spleen. However, expression of YcMMP-9 mRNA was induced by Aeromonas hydrophila stimulation, especially in these four tissues mentioned above. It indicated that YcMMP-9 was involved in innate immune responses against bacterial infection.

  16. 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.

  17. 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;…

  18. 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)

  19. Enhanced cyanophycin production by Escherichia coli overexpressing the heterologous cphA gene from a deep sea metagenomic library.

    PubMed

    Du, Jikun; Li, Li; Zhou, Shining

    2017-02-01

    Cyanophycin is a non-ribosomally synthesized polymer and its microbial production has attracted increased attention due to its pharmaceutical and chemical values. For the characterization and production of cyanophycin, the cphA49 gene was cloned and expressed in Escherichia coli. Soluble cyanophycin was isolated from the cultures and characterized. The results showed that it was composed of 50% of aspartic acid, 45% of arginine, and 3.5% of lysine, and exhibited a homogenous molecular mass of 35 kDa. To improve soluble cyanophycin production, the induction conditions for cphA49 gene expression were optimized. Meanwhile, the effects of medium content and induction duration on soluble cyanophycin production were also investigated, and the soluble cyanophycin yield reached a maximum at 72 h. Finally, to further increase the soluble cyanophycin production, the cultivation was carried out by supplement of arginine, aspartic acid, lysine and glucose into the minimal resource medium after cphA49 gene expression level was improved under optimized conditions, and the maximum concentration of soluble cyanophycin reached 1.72 g/L.

  20. Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds

    PubMed Central

    Yang, Yuzhan; Zhan, Aibin; Meng, Fanjuan; Xu, Wenbin

    2016-01-01

    Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to

  1. Construction of a Lotus japonicus late nodulin expressed sequence tag library and identification of novel nodule-specific genes.

    PubMed Central

    Szczyglowski, K; Hamburger, D; Kapranov, P; de Bruijn, F J

    1997-01-01

    A range of novel expressed sequence tags (ESTs) associated with late developmental events during nodule organogenesis in the legume Lotus japonicus were identified using mRNA differential display; 110 differentially displayed polymerase chain reaction products were cloned and analyzed. Of 88 unique cDNAs obtained, 22 shared significant homology to DNA/protein sequences in the respective databases. This group comprises, among others, a nodule-specific homolog of protein phosphatase 2C, a peptide transporter protein, and a nodule-specific form of cytochrome P450. RNA gel-blot analysis of 16 differentially displayed ESTs confirmed their nodule-specific expression pattern. The kinetics of mRNA accumulation of the majority of the ESTs analyzed were found to resemble the expression pattern observed for the L. japonicus leghemoglobin gene. These results indicate that the newly isolated molecular markers correspond to genes induced during late developmental stages of L. japonicus nodule organogenesis and provide important, novel tools for the study of nodulation. PMID:9276951

  2. Personal Virtual Libraries

    ERIC Educational Resources Information Center

    Pappas, Marjorie L.

    2004-01-01

    Virtual libraries are becoming more and more common. Most states have a virtual library. A growing number of public libraries have a virtual presence on the Web. Virtual libraries are a growing addition to school library media collections. The next logical step would be personal virtual libraries. A personal virtual library (PVL) is a collection…

  3. 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…

  4. Functional screening of a cDNA library from the desiccation-tolerant plant Selaginella lepidophylla in yeast mutants identifies trehalose biosynthesis genes of plant and microbial origin.

    PubMed

    Pampurova, Suzana; Verschooten, Katrien; Avonce, Nelson; Van Dijck, Patrick

    2014-11-01

    Trehalose is a non-reducing disaccharide that accumulates to large quantities in microbial cells, but in plants it is generally present in very low, barely-detectible levels. A notable exception is the desiccation-tolerant plant Selaginella lepidophylla, which accumulates very high levels of trehalose in both the hydrated and dehydrated state. As trehalose is known to protect membranes, proteins, and whole cells against dehydration stress, we have been interested in the characterization of the trehalose biosynthesis enzymes of S. lepidophylla; they could assist in engineering crop plants towards better stress tolerance. We previously isolated and characterized trehalose-6-phosphate synthases from Arabidopsis thaliana (desiccation sensitive) and S. lepidophylla (desiccation tolerant) and found that they had similar enzymatic characteristics. In this paper, we describe the isolation and characterization of trehalose-6-phosphate phosphatase from S. lepidophylla and show that its catalytic activities are also similar to those of its homolog in A. thaliana. Screening of an S. lepidophylla cDNA library using yeast trehalose biosynthesis mutants resulted in the isolation of a large number of trehalose biosynthesis genes that were of microbial rather than plant origin. Thus, we suggest that the high trehalose levels observed in S. lepidophylla are not the product of the plant but that of endophytes, which are known to be present in this plant. Additionally, the high trehalose levels in S. lepidophylla are unlikely to account for its desiccation tolerance, because its drought-stress-sensitive relative, S. moellendorffii, also accumulated high levels of trehalose.

  5. Construction of a full-length cDNA Library from Chinese oak silkworm pupa and identification of a KK-42-binding protein gene in relation to pupa-diapause termination.

    PubMed

    Li, Yu-Ping; Xia, Run-Xi; Wang, Huan; Li, Xi-Sheng; Liu, Yan-Qun; Wei, Zhao-Jun; Lu, Cheng; Xiang, Zhong-Huai

    2009-06-24

    In this study we successfully constructed a full-length cDNA library from Chinese oak silkworm, Antheraea pernyi, the most well-known wild silkworm used for silk production and insect food. Total RNA was extracted from a single fresh female pupa at the diapause stage. The titer of the library was 5 x 10(5) cfu/ml and the proportion of recombinant clones was approximately 95%. Expressed sequence tag (EST) analysis was used to characterize the library. A total of 175 clustered ESTs consisting of 24 contigs and 151 singlets were generated from 250 effective sequences. Of the 175 unigenes, 97 (55.4%) were known genes but only five from A. pernyi, 37 (21.2%) were known ESTs without function annotation, and 41 (23.4%) were novel ESTs. By EST sequencing, a gene coding KK-42-binding protein in A. pernyi (named as ApKK42-BP; GenBank accession no. FJ744151) was identified and characterized. Protein sequence analysis showed that ApKK42-BP was not a membrane protein but an extracellular protein with a signal peptide at position 1-18, and contained two putative conserved domains, abhydro_lipase and abhydrolase_1, suggesting it may be a member of lipase superfamily. Expression analysis based on number of ESTs showed that ApKK42-BP was an abundant gene in the period of diapause stage, suggesting it may also be involved in pupa-diapause termination.

  6. Underground Libraries.

    ERIC Educational Resources Information Center

    Fuhlrott, Rolf

    1986-01-01

    Discussion of underground buildings constructed primarily during last two decades for various reasons (energy conservation, density of environment, preservation of landscape and historic buildings) notes advantages, disadvantages, and psychological and design considerations. Examples of underground libraries, built mainly in United States, are…

  7. Minnesota Zoological Garden Library.

    ERIC Educational Resources Information Center

    Norell, Angela

    1988-01-01

    Describes the history and functions of the Minnesota Zoological Garden library. Topics covered include the library collections; library services, including online search capabilities; and the various groups of users served by the library. (three references) (CLB)

  8. 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)

  9. 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…

  10. MicroRNA library screening identifies growth-suppressive microRNAs that regulate genes involved in cell cycle progression and apoptosis.

    PubMed

    Choi, Young-Chul; Yoon, Sena; Byun, Yuree; Lee, Gangtae; Kee, Honghwan; Jeong, Yongsu; Yoon, Jaeseung; Baek, Kwanghee

    2015-12-10

    Micro(mi)RNAs play important and varied roles in tumorigenesis; however, the full repertoire of miRNAs that affect cancer cell growth is not known. In this study, an miRNA library was screened to identify those that affect the growth of A549 tumor cells. Among 300 miRNAs, miR-28-5p, -323-5p, -510-5p, -552-3p, and -608 were the most effective in inhibiting cell growth. More specifically, overexpressing miR-28-5p, -323-5p, and -510-5p induced G1 arrest, as determined by flow cytometry, whereas that of miR-608 induced cell death in a caspase-dependent manner. Moreover, several genes involved in apoptosis and cell cycle progression were downregulated upon overexpression of each of the five miRNAs, with the functional targets of miR-552-3p and miR-608 confirmed by microarray, quantitative real-time PCR, and luciferase reporter assay. In miR-608-transfected cells, B cell lymphoma 2-like 1 (BCL2L1), D-type cyclin 1 (CCND1), CCND3, cytochrome b5 reductase 3 (CYB5R3), phosphoinositide 3-kinase regulatory subunit 2 (PIK3R2), specificity protein 1 (SP1), and phosphorylated Akt were all downregulated, while Bcl-2-interacting killer (BIK) was upregulated. Moreover, miR-608 was determined to have a suppressive function on tumor growth in an NCI-H460 xenograft model. These findings provide insights into the roles of five miRNAs in growth inhibition and their potential function as cancer therapeutics.

  11. Schistosoma japonicum: screening of cercariae cDNA library by specific single-chain antibody against SIEA26-28 ku and immunization experiment of the recombinant plasmids containing the selected genes.

    PubMed

    Gao, Dong-mei; Wang, Shi-ping; He, Zhuo; Fung, Ming-chiu; Liu, Ming-she; Yu, Lu-xin; Chen, Xiu-chun

    2010-06-01

    To obtain the gene encoding SIEA26-28 ku, which has been proven to be a potential anti-schistosomiasis vaccine candidate, screening Schistosoma japonicum (Sj) cercariae cDNA library with soluble specific single-chain antibody (SIEA26-28 ku-scFv) was performed. A large amount of specific single-chain antibody was harvested through construction of recombinant expression vector pET32a/scFv. The protein was purified and characterized. By using this protein (PET32a-scFv) as a probe, S. japonicum cercariae cDNA library was screened. Two strong positive clones were selected, and their eukaryotic recombinant plasmids were constructed. These genes were named as S. japonicum ribosomal protein S4 (SjRPS4) and S. japonicum ribosomal protein L7 (SjRPL7), respectively. Experiments of mice showed that both SjRPS4 and SjRPL7 DNA vaccines could induce significant immunoprotection. Result of these experiments further proved that the specific single-chain antibody is a very valuable tool in screening of cDNA library to get the corresponding molecules.

  12. Art Libraries Section. Special Libraries Division. Papers.

    ERIC Educational Resources Information Center

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

    Papers on art libraries, librarianship, and documentation presented at the 1982 International Federation of Library Associations (IFLA) conference include: (1) "The Tyranny of Distance: Art Libraries in Canada," a description by Mary F. Williamson of Canada's regional art libraries which serve both art students and the general public;…

  13. 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…

  14. Graph Library

    SciTech Connect

    Schulz, Martin; Arnold, Dorian

    2007-06-12

    GraphLib is a support library used by other tools to create, manipulate, store, and export graphs. It provides a simple interface to specifS’ arbitrary directed and undirected graphs by adding nodes and edges. Each node and edge can be associated with a set of attributes describing size, color, and shape. Once created, graphs can be manipulated using a set of graph analysis algorithms, including merge, prune, and path coloring operations. GraphLib also has the ability to export graphs into various open formats such as DOT and GML.

  15. 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.

  16. Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip and 16S rRNA gene clone library sequencing

    SciTech Connect

    Shankar Sagaram, U.; DeAngelis, K.M.; Trivedi, P.; Andersen, G.L.; Lu, S.-E.; Wang, N.

    2009-03-01

    relative abundance, species richness and phylogenetic diversity of the microbial communities associated with the leaf midribs of HLB symptomatic and asymptomatic citrus trees were investigated using high-density 16S rDNA microarray PhyloChip and 16S rRNA gene clone library methods.

  17. State Virtual Libraries

    ERIC Educational Resources Information Center

    Pappas, Marjorie L.

    2003-01-01

    Virtual library? Electronic library? Digital library? Online information network? These all apply to the growing number of Web-based resource collections managed by consortiums of state library entities. Some, like "INFOhio" and "KYVL" ("Kentucky Virtual Library"), have been available for a few years, but others are just starting. Searching for…

  18. 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)

  19. Genealogy and Libraries.

    ERIC Educational Resources Information Center

    Carothers, Diane Foxhill; And Others

    1983-01-01

    Ten articles describe genealogical collections of the National Archives and Library of Congress, state archives programs, academic research libraries, Allen County Public Library (Indiana), Newberry Library, Church of Jesus Christ of Latter-Day Saints genealogical library, and New England Historic Genealogical Society, and approaches to Black…

  20. 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…

  1. 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,…

  2. 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)

  3. Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning.

    PubMed

    Lehtonen, Soili I; Taskinen, Barbara; Ojala, Elina; Kukkurainen, Sampo; Rahikainen, Rolle; Riihimäki, Tiina A; Laitinen, Olli H; Kulomaa, Markku S; Hytönen, Vesa P

    2015-01-01

    Efficient and robust subcloning is essential for the construction of high-diversity DNA libraries in the field of directed evolution. We have developed a more efficient method for the subcloning of DNA-shuffled libraries by employing recombination cloning (Gateway). The Gateway cloning procedure was performed directly after the gene reassembly reaction, without additional purification and amplification steps, thus simplifying the conventional DNA shuffling protocols. Recombination-based cloning, directly from the heterologous reassembly reaction, conserved the high quality of the library and reduced the time required for the library construction. The described method is generally compatible for the construction of DNA-shuffled gene libraries.

  4. 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…

  5. 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…

  6. 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…

  7. The "Integrated Library System."

    ERIC Educational Resources Information Center

    Dowlin, Kenneth E.

    1985-01-01

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

  8. 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…

  9. Libraries and Learning

    ERIC Educational Resources Information Center

    Rainie, Lee

    2016-01-01

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

  10. 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…

  11. 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.

  12. Principles and application of antibody libraries for infectious diseases.

    PubMed

    Lim, Bee Nar; Tye, Gee Jun; Choong, Yee Siew; Ong, Eugene Boon Beng; Ismail, Asma; Lim, Theam Soon

    2014-12-01

    Antibodies have been used efficiently for the treatment and diagnosis of many diseases. Recombinant antibody technology allows the generation of fully human antibodies. Phage display is the gold standard for the production of human antibodies in vitro. To generate monoclonal antibodies by phage display, the generation of antibody libraries is crucial. Antibody libraries are classified according to the source where the antibody gene sequences were obtained. The most useful library for infectious diseases is the immunized library. Immunized libraries would allow better and selective enrichment of antibodies against disease antigens. The antibodies generated from these libraries can be translated for both diagnostic and therapeutic applications. This review focuses on the generation of immunized antibody libraries and the potential applications of the antibodies derived from these libraries.

  13. Summer library reading programs.

    PubMed

    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 summarizes some of the research in the field and relates it to library programs and usage by students. Several traditional and innovative programs from U.S. and Canadian libraries are described. She concludes with a call for further research related to summer library reading programs.

  14. OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis.

    PubMed

    Tarkka, Mika T; Herrmann, Sylvie; Wubet, Tesfaye; Feldhahn, Lasse; Recht, Sabine; Kurth, Florence; Mailänder, Sarah; Bönn, Markus; Neef, Maren; Angay, Oguzhan; Bacht, Michael; Graf, Marcel; Maboreke, Hazel; Fleischmann, Frank; Grams, Thorsten E E; Ruess, Liliane; Schädler, Martin; Brandl, Roland; Scheu, Stefan; Schrey, Silvia D; Grosse, Ivo; Buscot, François

    2013-07-01

    Oaks (Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags (ESTs) have been characterized in ectomycorrhizal (EM) symbioses. We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone (DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum. Using the Mimicking Intelligent Read Assembly (MIRA) and Trinity assembler, the OakContigDF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated. In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees.

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

    ERIC Educational Resources Information Center

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

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

  16. The Virtual Library: Computers in Libraries Canada.

    ERIC Educational Resources Information Center

    Saunders, Laverna

    1992-01-01

    Reports on a postconference workshop on virtual libraries that was presented at the third annual Computers in Libraries Canada Conference. Highlights include networks; technological change; administrative issues, including organizational structure, staff training, strategic planning, and financial resources; a case study of the University of…

  17. 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"…

  18. Administrative Libraries Section. Special Libraries Division. Papers.

    ERIC Educational Resources Information Center

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

    Six papers on the theme, "Administrative Libraries in a Technological World: Past, Present, and Future--A General Stocktaking and a State of the Art Report" focus on West German telecommunications and information technology and the use of data processing and other technological aids in West German administrative libraries. These papers,…

  19. 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);…

  20. Community, Library, and Revolution

    ERIC Educational Resources Information Center

    Freiser, Leonard H.

    1970-01-01

    Discusses the need for greatly expanded community library services, for librarians to accept social responsibility for education and information, and for the library to become a program for getting information to where it is needed. (JS)

  1. 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)

  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. Small Libraries, Big Technology

    ERIC Educational Resources Information Center

    Roberts,Gary

    2005-01-01

    Small libraries don't have the resources to adopt every new technology. It is important that small libraries operate strategically, adopting only those technologies that are the most beneficial to their patrons.

  4. Novel Informatic Approaches to Analyze Gene Expression Data with the ToxCast 320 Chemical Library in Cultures of Primary Human Hepatocytes

    EPA Science Inventory

    Prevailing methodologies in the analysis of gene expression data often neglect to incorporate full concentration and time response due to limitations in throughput and sensitivity with traditional microarray approaches. We have developed a high throughput assay suite using primar...

  5. New York Zoological Society Library.

    ERIC Educational Resources Information Center

    Johnson, Steven P.

    1988-01-01

    Describes the institutional setting, history, and services of the New York Zoological Society Library. Topics covered include clientele; library collections and special collections; library staffing and organizational structure; computer applications; and relationships with other libraries. (11 references) (CLB)

  6. Comprehensive transposon mutant library of Pseudomonas aeruginosa

    PubMed Central

    Jacobs, Michael A.; Alwood, Ashley; Thaipisuttikul, Iyarit; Spencer, David; Haugen, Eric; Ernst, Stephen; Will, Oliver; Kaul, Rajinder; Raymond, Christopher; Levy, Ruth; Chun-Rong, Liu; Guenthner, Donald; Bovee, Donald; Olson, Maynard V.; Manoil, Colin

    2003-01-01

    We have developed technologies for creating saturating libraries of sequence-defined transposon insertion mutants in which each strain is maintained. Phenotypic analysis of such libraries should provide a virtually complete identification of nonessential genes required for any process for which a suitable screen can be devised. The approach was applied to Pseudomonas aeruginosa, an opportunistic pathogen with a 6.3-Mbp genome. The library that was generated consists of 30,100 sequence-defined mutants, corresponding to an average of five insertions per gene. About 12% of the predicted genes of this organism lacked insertions; many of these genes are likely to be essential for growth on rich media. Based on statistical analyses and bioinformatic comparison to known essential genes in E. coli, we estimate that the actual number of essential genes is 300-400. Screening the collection for strains defective in two defined multigenic processes (twitching motility and prototrophic growth) identified mutants corresponding to nearly all genes expected from earlier studies. Thus, phenotypic analysis of the collection may produce essentially complete lists of genes required for diverse biological activities. The transposons used to generate the mutant collection have added features that should facilitate downstream studies of gene expression, protein localization, epistasis, and chromosome engineering. PMID:14617778

  7. Comprehensive transposon mutant library of Pseudomonas aeruginosa.

    PubMed

    Jacobs, Michael A; Alwood, Ashley; Thaipisuttikul, Iyarit; Spencer, David; Haugen, Eric; Ernst, Stephen; Will, Oliver; Kaul, Rajinder; Raymond, Christopher; Levy, Ruth; Chun-Rong, Liu; Guenthner, Donald; Bovee, Donald; Olson, Maynard V; Manoil, Colin

    2003-11-25

    We have developed technologies for creating saturating libraries of sequence-defined transposon insertion mutants in which each strain is maintained. Phenotypic analysis of such libraries should provide a virtually complete identification of nonessential genes required for any process for which a suitable screen can be devised. The approach was applied to Pseudomonas aeruginosa, an opportunistic pathogen with a 6.3-Mbp genome. The library that was generated consists of 30,100 sequence-defined mutants, corresponding to an average of five insertions per gene. About 12% of the predicted genes of this organism lacked insertions; many of these genes are likely to be essential for growth on rich media. Based on statistical analyses and bioinformatic comparison to known essential genes in E. coli, we estimate that the actual number of essential genes is 300-400. Screening the collection for strains defective in two defined multigenic processes (twitching motility and prototrophic growth) identified mutants corresponding to nearly all genes expected from earlier studies. Thus, phenotypic analysis of the collection may produce essentially complete lists of genes required for diverse biological activities. The transposons used to generate the mutant collection have added features that should facilitate downstream studies of gene expression, protein localization, epistasis, and chromosome engineering.

  8. Library Community Services.

    ERIC Educational Resources Information Center

    Correy, Therese; And Others

    Services to the elderly, institutionalized, and physically and mentally exceptional, who are unable to use the public library in its traditional form, are described in this guide to programs at the Inglewood (California) Public Library. Topics include: (1) overall library goals and activities; (2) functional and organizational structure of…

  9. 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)

  10. School Library Policy Statement.

    ERIC Educational Resources Information Center

    Manitoba Dept. of Education, Winnipeg. Instructional Resources Branch.

    The School Library Policy Statement for Manitoba schools begins with the mission statement of Manitoba Education and Training and the Goals of Learning for Manitoba. Statements of Manitoba's School Library Policy and the Philosophy of the School Library Program are also provided, together with an outline of the responsibilities of both Manitoba's…

  11. Virtual Libraries: Service Realities.

    ERIC Educational Resources Information Center

    Novak, Jan

    2002-01-01

    Discussion of changes in society that have resulted from information and communication technologies focuses on changes in libraries and a new market for library services with new styles of clients. Highlights client service issues to be considered when transitioning to a virtual library situation. (Author/LRW)

  12. 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)

  13. The Occasional Library Newsletter

    ERIC Educational Resources Information Center

    Gustafson, Chris

    2004-01-01

    An important tool for communication and collaboration is the library newsletter, which the library media specialist writes to the staff, teachers and library media specialist from other schools. The newsletter includes upcoming events teachers can sign up for, information on web sites to be used for projects, curriculum ideas, introduction of a…

  14. 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…

  15. 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.

  16. Tomorrow's Library Today.

    ERIC Educational Resources Information Center

    Penniman, W. David

    1987-01-01

    Presents a model for predicting and shaping the impact of information technologies on libraries and the library role which is based on the effects of computerization in various business applications. The library network at AT&T Bell Laboratories is described as an example of a successful implementation of the model. (CLB)

  17. Place as Library?

    ERIC Educational Resources Information Center

    Davenport, Nancy

    2006-01-01

    Digital technology is redrawing the library's blueprint. Planners are thinking in new ways about how to design libraries as places for learning rather than primarily as storehouses of information. This thinking has given rise to much discussion--and to many publications--about the "library as place." In this article, the author asks why not also…

  18. 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…

  19. 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.…

  20. 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…

  1. Digital Libraries: An Overview.

    ERIC Educational Resources Information Center

    Schwartz, Candy

    2000-01-01

    Provides an overview of the basic components of a digital library. Highlights include library collections; metadata; services, including information seeking and retrieval, reference query fulfillment, and user training; user interaction with digital libraries, including searching, browsing, and navigation; economic support; maintenance;…

  2. 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…

  3. 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…

  4. LIBRARY SYSTEMS ANALYSIS.

    ERIC Educational Resources Information Center

    HIEBER, CAROLINE E.; TAYLOR, ROBERT S.

    STEPS THAT THE LIBRARY CAN TAKE IN PREPARING FOR A CHANGE TO AN AUTOMATED SYSTEM WERE INVESTIGATED. THE METHOD DESCRIBED WAS BASED ON AN ANALYSIS OF CLERICAL AND OFFICE WORK CALLED INTEGRATED PROCEDURES OF CONTROL (IPC). THE APPLICATION OF LIBRARY SYSTEMS ANALYSIS (LISA) TO THE LEHIGH UNIVERSITY LIBRARY IS DESCRIBED. THIS PROCESS INVOLVED (1)…

  5. Library Journal Classics.

    ERIC Educational Resources Information Center

    Crunden, Frederick; And Others

    1993-01-01

    Includes four articles originally published in the 1890s. Highlights include a discussion of freedom of speech, political opinions, and the role of the public library in social reform; the establishment of a congressional or national library; censorship in libraries; and a criticism of a librarian by his assistant. (LRW)

  6. Library Journal Classics.

    ERIC Educational Resources Information Center

    Berninghausen, David; And Others

    1993-01-01

    Provides excerpts from David Berninghausens's "Social Responsibility vs. the Library Bill of Rights" and responses that appeared in "Library Journal" in 1972 and 1973 because of the continuing debate over the role of the American Library Association (ALA) Social Responsibilities Round Table and whether or not ALA should take…

  7. 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…

  8. Library Building and Design.

    ERIC Educational Resources Information Center

    Jones, David J.; Gordon, Heather; Caddy, Julie; Kahlert, Maureen; Johnson, Carolyn; Holdstock, Fiona

    1997-01-01

    More frequently, community connections are being expressed in library design briefs and reflected in the completed buildings. This collection of brief articles discusses community involvement in library design and services and describes library construction projects in Australia and Malaysia. Also, discusses community art programs, integrating…

  9. 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…

  10. 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…

  11. 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…

  12. Concepts of Library Goodness.

    ERIC Educational Resources Information Center

    Buckland, Michael K.

    1982-01-01

    Orr's schema for measuring the quality and value of libraries is described and discussed with respect to three paradoxes--the evaluation of catalogs, optimal library size, and Lenin's view of public libraries in the U.S. Seven references are cited. (CHC)

  13. 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…

  14. 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…

  15. 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…

  16. Synthetic promoter libraries for Corynebacterium glutamicum.

    PubMed

    Rytter, Jakob Vang; Helmark, Søren; Chen, Jun; Lezyk, Mateusz Jakub; Solem, Christian; Jensen, Peter Ruhdal

    2014-03-01

    The ability to modulate gene expression is an important genetic tool in systems biology and biotechnology. Here, we demonstrate that a previously published easy and fast PCR-based method for modulating gene expression in lactic acid bacteria is also applicable to Corynebacterium glutamicum. We constructed constitutive promoter libraries based on various combinations of a previously reported C. glutamicum -10 consensus sequence (gngnTA(c/t)aaTgg) and the Escherichia coli -35 consensus, either with or without an AT-rich region upstream. A promoter library based on consensus sequences frequently found in low-GC Gram-positive microorganisms was also included. The strongest promoters were found in the library with a -35 region and a C. glutamicum -10 consensus, and this library also represents the largest activity span. Using the alternative -10 consensus TATAAT, which can be found in many other prokaryotes, resulted in a weaker but still useful promoter library. The upstream AT-rich region did not appear to affect promoter strength in C. glutamicum. In addition to the constitutive promoters, a synthetic inducible promoter library, based on the E. coli lac-promoter, was constructed by randomizing the 17-bp spacer between -35 and -10 consensus sequences and the sequences surrounding these. The inducible promoter library was shown to result in β-galactosidase activities ranging from 284 to 1,665 Miller units when induced by IPTG, and the induction fold ranged from 7-59. We find that the synthetic promoter library (SPL) technology is convenient for modulating gene expression in C. glutamicum and should have many future applications, within basic research as well as for optimizing industrial production organisms.

  17. Csa-19, a radiation-responsive human gene, identified by an unbiased two-gel cDNA library screening method in human cancer cells

    NASA Technical Reports Server (NTRS)

    Balcer-Kubiczek, E. K.; Meltzer, S. J.; Han, L. H.; Zhang, X. F.; Shi, Z. M.; Harrison, G. H.; Abraham, J. M.

    1997-01-01

    A novel polymerase chain reaction (PCR)-based method was used to identify candidate genes whose expression is altered in cancer cells by ionizing radiation. Transcriptional induction of randomly selected genes in control versus irradiated human HL60 cells was compared. Among several complementary DNA (cDNA) clones recovered by this approach, one cDNA clone (CL68-5) was downregulated in X-irradiated HL60 cells but unaffected by 12-O-tetradecanoyl phorbol-13-acetate, forskolin, or cyclosporin-A. DNA sequencing of the CL68-5 cDNA revealed 100% nucleotide sequence homology to the reported human Csa-19 gene. Northern blot analysis of RNA from control and irradiated cells revealed the expression of a single 0.7-kilobase (kb) messenger RNA (mRNA) transcript. This 0.7-kb Csa-19 mRNA transcript was also expressed in a variety of human adult and corresponding fetal normal tissues. Moreover, when the effect of X- or fission neutron-irradiation on Csa-19 mRNA was compared in cultured human cells differing in p53 gene status (p53-/- versus p53+/+), downregulation of Csa-19 by X-rays or fission neutrons was similar in p53-wild type and p53-null cell lines. Our results provide the first known example of a radiation-responsive gene in human cancer cells whose expression is not associated with p53, adenylate cyclase or protein kinase C.

  18. 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…

  19. 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.

  20. Microbial diversity in polluted harbor sediments II: Sulfate-reducing bacterial community assessment using terminal restriction fragment length polymorphism and clone library of dsrAB gene

    NASA Astrophysics Data System (ADS)

    Zhang, Wen; Song, Lin-sheng; Ki, Jang-Seu; Lau, Chun-Kwan; Li, Xiang-Dong; Qian, Pei-Yuan

    2008-02-01

    Sulfate-reducing bacteria (SRB) are important regulators of a variety of processes in coastal marine sediments regarding organic matter turnover, biodegradation of pollutants, and sulfur and carbon cycles. Yet their community compositions have not been investigated in polluted harbor sediments. This study described the diversity and spatial variation of SRB communities in surface sediments in Victoria Harbor, Hong Kong. The spatial variation of SRB communities was described by terminal restriction fragment length polymorphism (T-RFLP). The results showed that the most diversified terminal restriction fragments were found at polluted sites. In addition, cluster analysis indicated that although the SRB communities were different at the two polluted sites, they were still more similar to each other than to the two more distant reference sites. Based on a dsrAB clone library constructed at a polluted site, diversified SRB were found, represented by 30 Operational Taxonomic Units (OTUs). Upon comparisons among the SRB sequences detected from this study and those in the GenBank, five clades of SRB were found. Three clades belonged to the known families Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteriaceae. The majority of sequenced clones, which distantly related to sequences in the GenBank, constituted the remaining two unclassified groups, suggesting unique SRB members related to the polluted harbor environment. Statistical analyses indicated that estimated SRB richness correlated with environment factors such as sulfur content, acid volatile sulfate, and redox potential.

  1. Integration of Library Services in the System of Digital Libraries

    NASA Astrophysics Data System (ADS)

    Bezdushnyj, A. N.; Kalenov, N. E.; Kouriv, P. M.; Serebryakov, V. A.

    The article is devoted to the functional extension of the Integrated System of Information Resources of RAS (ISIR RAS - RFBR 99-07-90139 project). This extension (Library Subsystem) provides integration of library services in ISIR RAS electronic libraries system. Library Subsystem implements standard library services such as information about free and ordered copies of editions, creation of the library orders for edition etc. The Library Subsystem is an integrated solution; it's based on ISIR data model and technologies.

  2. Broilers fed dietary vitamins harbor higher diversity of cecal bacteria and higher ratio of Clostridium, Faecalibacterium, and Lactobacillus than broilers with no dietary vitamins revealed by 16S rRNA gene clone libraries.

    PubMed

    Luo, Yu-heng; Peng, Huan-wei; Wright, André-Denis G; Bai, Shi-ping; Ding, Xue-mei; Zeng, Qiu-feng; Li, Hua; Zheng, Ping; Su, Zhuo-wei; Cui, Ren-yong; Zhang, Ke-ying

    2013-09-01

    Research on the interaction between dietary vitamins and intestinal bacteria is poorly understood. To investigate the effect of dietary vitamins on the cecal bacterial communities, 2 bacterial 16S rRNA gene clone libraries were constructed from pooled PCR products obtained from the cecal digesta of 28-d broilers fed diets with vitamins (V) at the NRC level or with no vitamins (NV). The results showed that BW gain and average feed intake of V broilers was significantly higher (P < 0.01) than NV broilers, whereas the feed/gain ratio was significantly lower (P < 0.01) in V broilers. A total of 188 and 185 clones were sequenced for the NV and V broilers, respectively. Sequence identity criterion of 98% was used to assign sequences to operational taxonomic units (OTU). Clones from the NV group broilers were assigned to 14 OTU, with 33% clones affiliated with the genus Clostridium, 19% affiliated with the genera Escherichia/Shigella, 14% affiliated with the genus Bacteroides, and the remaining clones (34%) affiliated with 5 other bacterial genera (Faecalibacterium, Parasporobacterium, Ruminococcus, Streptococcus, and Subdoligranulum). Clones from the V group broilers were assigned to 23 OTU, with 46% of the clones affiliated with the genus Clostridium, 11% affiliated with the genus Fecalibacterium, and the remaining clones (43%) affiliated with 8 other genera (Anaerofilum, Lactobacillus, Anaerotruncus, Oscillibacter, Alistipes, Gracilibacter, Acetivibrio, and Haloplasma). Three OTU assigned to Clostridium, Faecalibacterium, and Ruminoccus were shared between the 2 libraries. Shannon diversity index showed the V broilers exhibited significantly higher bacterial diversity (P = 0.05), and Libshuff analysis indicated that the community structure between the 2 groups was significantly different (P < 0.0001). These results suggest that lack of dietary vitamins can increase the ratio of facultative pathogenic bacteria and decrease the diversity of bacteria in the cecum of

  3. Biosynthetic Functional Gene Analysis of Bis-Indole Metabolites from 25D7, a Clone Derived from a Deep-Sea Sediment Metagenomic Library

    PubMed Central

    Yan, Xia; Tang, Xi-Xiang; Qin, Dan; Yi, Zhi-Wei; Fang, Mei-Juan; Wu, Zhen; Qiu, Ying-Kun

    2016-01-01

    This work investigated the metabolites and their biosynthetic functional hydroxylase genes of the deep-sea sediment metagenomic clone 25D7. 5-Bromoindole was added to the 25D7 clone derived Escherichia coli fermentation broth. The new-generated metabolites and their biosynthetic byproducts were located through LC-MS, in which the isotope peaks of brominated products emerged. Two new brominated bis-indole metabolites, 5-bromometagenediindole B (1), and 5-bromometagenediindole C (2) were separated under the guidance of LC-MS. Their structures were elucidated on the basis of 1D and 2D NMR spectra (COSY, HSQC, and HMBC). The biosynthetic functional genes of the two new compounds were revealed through LC-MS and transposon mutagenesis analysis. 5-Bromometagenediindole B (1) also demonstrated moderately cytotoxic activity against MCF7, B16, CNE2, Bel7402, and HT1080 tumor cell lines in vitro. PMID:27258289

  4. Transposase mediated construction of RNA-seq libraries.

    PubMed

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

    2012-01-01

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

  5. Academic Libraries, 2000. E.D. Tabs.

    ERIC Educational Resources Information Center

    Carey, Nancy; Justh, Natalie M.; Williams, Jeffrey W.

    This report discusses the state of academic libraries in 2000. It defines "academic library" as well as discusses library services, library collections, library staff, library expenditures, and electronic services. (Author/AMT)

  6. A Directory of Library Instruction Programs in Indiana Academic Libraries.

    ERIC Educational Resources Information Center

    Skinner, Jane, Comp.; Violette, Judith, Comp.

    A survey of 40 reporting academic libraries in Indiana developed this directory of library user instruction programs which provides an index profile of library resources and types of programs within the state. Entries are alphabetical in outline form and provide a library contact person, capsule information about the library instruction program,…

  7. Standards for Medical Library Technicians, Medical Library Association.

    ERIC Educational Resources Information Center

    Medical Library Association, Chicago, IL.

    A medical library technician is a semiprofessional library employee whose duties require knowledge and skill based on a minimum of two years' general college education that includes library instruction beyond the clerical level. The medical library technician must have a practical knowledge of library functions and services, an understanding of…

  8. 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.

  9. 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.

  10. NEIC Library Services

    EPA Pesticide Factsheets

    The National Enforcement Investigation Center (NEIC) Environmental Forensic Library partners with NEIC's forensic scientists to retrieve, validate and deliver information to develop methods, defensible regulations, and environmental measurements.

  11. Automated Library System Specifications.

    DTIC Science & Technology

    1986-06-01

    AD-A78 95 AUTOMATED LIBRARY SYSTEM SPECIFICATIONS(U) ARMY LIBRARY /i MANAGEMENT OFFICE ALEXANDRIA VA ASSISTANT CHIEF OF STAFF FOR INFORMATION... MANAGEMENT M B BONNETT JUN 86 UNCLASSIFIED F/G 9/2 NLEElIIhllEEEEE IllEEEEEllllEI .1lm lliml * ~I fI.L25 MI, [OCM RL,;OCLUTO fl. ’N k~ AUTOMATED LIBRARY...SYSTEM SPECIFICATIONS .,I Prepared by Mary B. Bonnett ARMY LIBRARY MANAGEMENT OFFICE OFFICE OF THE ASSISTANT CHIEF OF STAFF FOR INFORMATION MANAGEMENT Lij

  12. IView: Introgression library visualization and query tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Near-isogenic lines (NIL) are powerful genetic resources to analyze phenotypic variation and are important to map-base clone genes underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. We have created a tool ...

  13. Generation of Arabidopsis mutants by heterologous expression of a full length cDNA library from tomato fruits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heterologous expression of cDNA libraries in Arabidopsis and other plants has been used for gene identifications. To identify functions of tomato genes, we expressed a tomato full-length cDNA library in Arabidopsis thaliana and generated over 7,000 mutants. We constructed a tomato cDNA library with ...

  14. Houston Cole Library Policy Manual.

    ERIC Educational Resources Information Center

    Henderson, William Abbot, Ed.

    This policy manual of Jacksonville State University's Houston Cole Library serves as a statement of the library's mission, goals, and objectives; an interpretive guide for library faculty, staff, and students; and informational document for library patrons concerning the library's programs and policies. The contents include the following:…

  15. 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…

  16. 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.

  17. Future-Proof Your Library

    ERIC Educational Resources Information Center

    Miller, Rebecca

    2008-01-01

    This article presents an excerpt of Library Journal's (LJ's) Movers & Shakers ideas on how to ensure a vital library for the future. Several identify a disconnect between what librarians and libraries do and what users think they do. Mending this gap, they say, would transform library recruitment and library support. While specific insights on…

  18. Wisconsin Library Service Record, 1978.

    ERIC Educational Resources Information Center

    Wisconsin State Dept. of Public Instruction, Madison. Div. of Library Services.

    Narrative description and updated statistical tables cover all types of libraries and library related activities in the state. Major areas reported on are the Wisconsin library network, including planning, media services, and special services for children, the institutionalized, and handicapped; library and media organizations; library education,…

  19. Wisconsin Library Service Record, 1974.

    ERIC Educational Resources Information Center

    Wisconsin State Dept. of Public Instruction, Madison. Div. of Library Services.

    In a record of library activities in Wisconsin in 1974, the activities of the Division for Library Services are described along with the Wisconsin Library Network and the state and regional library networks, services, and resources. Lists of library and media organizations and education programs are followed by a directory of academic, public,…

  20. A Tale of Two Libraries.

    ERIC Educational Resources Information Center

    Martinez, Ed

    1999-01-01

    Reviews the profiles of a typical public library, the Redondo Beach Public Library (California), and its nearby community college library, the Schauerman Library at El Camino College in Torrance, California. Discusses similarities between staff in public and academic libraries; differences between the two environments; and like missions of both…

  1. Central Statistical Libraries in Europe.

    ERIC Educational Resources Information Center

    Kaiser, Lisa

    The paper tries to clarify the position special governmental libraries hold in the system of libraries of today by investigating only one specific type of library mainly from a formal and historical point of view. Central statistical libraries in Europe were first regarded as administrative and archival libraries. Their early holdings of foreign…

  2. Suggestions for Library Network Design.

    ERIC Educational Resources Information Center

    Salton, Gerald

    1979-01-01

    Various approaches to the design of automatic library systems are described, suggestions for the design of rational and effective automated library processes are posed, and an attempt is made to assess the importance and effect of library network systems on library operations and library effectiveness. (Author/CWM)

  3. 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…

  4. Genes

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Genes URL of this page: //medlineplus.gov/ency/article/ ...

  5. Libraries in Mauritius: Ideal Size for a National Library Service.

    ERIC Educational Resources Information Center

    Harrison, K. C.

    1978-01-01

    A UNESCO consultant describes services provided by academic, public, and school libraries in Mauritius, and discusses levels of professionalism and salaries of librarians, opportunities for library education, and the possibility of developing a national library service. (JAB)

  6. 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...

  7. Construction and analysis of antennal cDNA library from rice striped stem borer, Chilo suppressalis (Walker) (Lepidoptera: Pyralidae), and expression profiles of putative odorant-binding protein and chemosensory protein genes.

    PubMed

    Gong, Zhong-Jun; Liu, Su; Jiang, Yan-Dong; Zhou, Wen-Wu; Liang, Qing-Mei; Cheng, Jiaan; Zhang, Chuan-Xi; Zhu, Zeng-Rong; Gurr, Geoff M

    2015-05-01

    In this study, we constructed a high-quality cDNA library from the antennae of the Chilo suppressalis (Walker) (Lepidoptera: Pyralidae). A total of 1,235 colonies with inserts greater than 0.7 kb were sequenced and analyzed. Homology searching coupled with bioinformatics analysis identified 15 and 7 cDNA sequences, respectively, encoding putative odorant-binding proteins (OBPs) and chemosensory proteins (CSPs). A phylogenetic tree of CsupCSPs showed that each CsupCSP has orthologs in Manduca sexta and Bombyx mori with strong bootstrapping support. One CSP was either very specific or more related to the CSPs of another species than to conspecific CSP. The expression profiles of the OBPs and CSPs in different tissues were measured by real-time quantitative PCR. The results revealed that of the 11 OBP genes, the transcript levels of CsupOBP1, CsupOBP5, and CsupOBP7 were higher in both male and female antennae than those in other tissues. And CsupCSP7 was highly expressed in both male and female antennae. Based on these results, the possible physiological functions of CsupOBPs and CsupCSPs were discussed.

  8. Multipurpose Transposon-Insertion Libraries in Yeast.

    PubMed

    Kumar, Anuj

    2016-06-01

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

  9. 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…

  10. 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)

  11. Library Media Services Handbook.

    ERIC Educational Resources Information Center

    Winnipeg School Div. Number 1, Manitoba (Canada).

    This 1991 edition of the handbook for Winnipeg School Division Number 1 school library media programs presents detailed program guidelines, objectives, philosophies, and goals in five major sections: (1) Library Policy and Practices (statement of the division's educational philosophy and goals, philosophy and goals of the division's library…

  12. Planning for Library Excellence.

    ERIC Educational Resources Information Center

    Virginia State Library and Archives, Richmond.

    Intended to be used by librarians, this guide will also be useful to boards of trustees, governing officials, members of funding agencies, and community support groups involved in planning on a local level and within the context of regional and state library service. It provides information to help libraries plan and evaluate their services and…

  13. The Jimmy Carter Library.

    ERIC Educational Resources Information Center

    Schewe, Donald B.

    1989-01-01

    Reviews past approaches to the preservation of Presidential papers, the development of the system of Presidential Libraries, and the development of the Jimmy Carter Library. The National Archives' approach to computerization to deal with the increasing volume of materials is detailed and the PresNet computerized information system is described.…

  14. 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…

  15. Trotsky's Vision of Libraries.

    ERIC Educational Resources Information Center

    Baker, William; Hurych, Jitka

    1991-01-01

    Discusses Leon Trotsky's views on libraries, librarians, and librarianship in Soviet society in the 1920s as expressed in a speech, "Leninism and Library Work." Topics discussed include role of librarian in promoting literacy, including the use of maps and reference books to explain newspaper stories; the selection of books; and fighting…

  16. 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…

  17. 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…

  18. 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.

  19. 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.…

  20. Stress in the Library.

    ERIC Educational Resources Information Center

    Bunge, Charles

    1987-01-01

    Reports results of a survey of 800 library staff members on aspects of library work that they find stressful. The findings include sources of satisfaction and stress for all participants, and sources of stress specific to public services librarians, technical services librarians, and support staff members. (CLB)

  1. 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…

  2. 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…

  3. Revolution and the Library.

    ERIC Educational Resources Information Center

    Gorniak-Kocikowska, Krystyna

    2001-01-01

    Considers the impact that the computer revolution has had on college and university libraries. Discusses the historical background of changes that resulted from the invention of the printing press; the development of national languages; knowledge acquisition; the historical role of religion; content control of libraries; and changes in students.…

  4. Libraries of the Future.

    ERIC Educational Resources Information Center

    McKenzie, Jamie

    1996-01-01

    Predicts the effects of information technology (IT) on libraries of the future. Discusses negative implications for school libraries. Describes four emerging roles for media specialists: (1) showing students and staff how to navigate information networks; (2) teaching users how to evaluate and select information; (3) designing information systems;…

  5. Keeping Libraries Open.

    ERIC Educational Resources Information Center

    Franklin, Hardy R.

    Major social institutions repeatedly reinforce the deprivation of the urban disadvantaged. Libraries, as the "Universities of the People," must commit themselves to the promotion of a better standard of life for all people, especially the poor. A close look at priorities is especially important if libraries are to pursue their mission in…

  6. 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)

  7. 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)

  8. Library Laws of Texas.

    ERIC Educational Resources Information Center

    Seidenberg, Ed, Ed.

    Compiled to provide a central reference point for all legislative information pertaining to libraries in the state of Texas, this publication includes all pertinent legislation as amended through the 66th Legislature, Regular Session, 1979. It contains articles dealing specifically with archives, buildings and property, city libraries, non-profit…

  9. 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…

  10. 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…

  11. 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…

  12. 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."

  13. Integrated library systems.

    PubMed Central

    Goldstein, C M

    1983-01-01

    The development of integrated library systems is discussed. The four major discussion points are (1) initial efforts; (2) network resources; (3) minicomputer-based systems; and (4) beyond library automation. Four existing systems are cited as examples of current systems. PMID:6354321

  14. Library Instruction Program Proposal.

    ERIC Educational Resources Information Center

    Cassata, Mary B.

    A number of studies cited in the literature show a positive correlation between the students scholastic grade point average and his library usage. The case is made by a growing cult of librarians who are engaged in "teaching the library" that the librarian so engaged makes a direct contribution to the student's success at his studies. Although…

  15. Prison Libraries: Bibliography.

    ERIC Educational Resources Information Center

    Gillespie, David M.

    An Alphabetically arranged bibliography, listing 485 entries representing 518 citations taken from "Poole's Index to Periodical Literature" 1802-1906, "Cannon's Bibliography of Library Economy," and "Library Literature" 1921 to mid-1970. Other sources used include: The Index to the Journal of Correctional Education; ten bibliographies taken from…

  16. "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…

  17. 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,…

  18. 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…

  19. 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…

  20. Iranian Special Library Standards.

    ERIC Educational Resources Information Center

    Harvey, John F.

    The purposes of these standards are: (1) to suggest the steps necessary for the establishment of special libraries; (2) for those recently established, to suggest the steps necessary to achieve satisfactory performance levels in all areas, and finally, (3) for well established libraries, to suggest the steps necessary to achieve excellence. These…

  1. 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)

  2. Guide to Library Automation.

    ERIC Educational Resources Information Center

    Toohill, Barbara G.

    Directed toward librarians and library administrators who wish to procure automated systems or services for their libraries, this guide offers practical suggestions, advice, and methods for determining requirements, estimating costs and benefits, writing specifications procuring systems, negotiating contracts, and installing systems. The advice…

  3. 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…

  4. Weeding Library Collections.

    ERIC Educational Resources Information Center

    Slote, Stanley J.

    This work, based on two recent research projects in the weeding of library collections and the identification of core collections, provides a comprehensive summary of the literature and research on these topics. It also presents practical guidance in weeding for the professional librarian or for the library school student. The book is divided into…

  5. 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…

  6. 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.

  7. Libraries and Lenin.

    ERIC Educational Resources Information Center

    Lynn, Karen

    This instructional unit combines a study of the Soviet leader V. I. Lenin with a study of libraries. Lenin was selected as the focus because of his support of books and libraries and because he oversaw a revolution that altered the political and social structure of Russia and the balance of power throughout the world. Included are lesson plan…

  8. 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…

  9. 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…

  10. Literacy Projects in Libraries.

    ERIC Educational Resources Information Center

    Gaughan, Karen K.

    1986-01-01

    Literacy Volunteers of America is described as a grassroots effort that has grown to national proportions. An overview of its development and case studies of library literacy projects in various states are provided, and recommendations are made for continued and future library participation in the literacy effort. (EM)

  11. 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…

  12. Academic Library Consortia in Transition.

    ERIC Educational Resources Information Center

    Alberico, Ralph

    2002-01-01

    Using the example of the Virtual Library of Virginia, describes how library consortia are in a state of transformation as technology enables the development of virtual libraries while expanding opportunities for sharing printed works. (EV)

  13. EPA Library Network Communication Strategies

    EPA Pesticide Factsheets

    To establish Agency-wide procedures for the EPA National Library Network libraries to communicate, using a range of established mechanisms, with other EPA libraries, EPA staff, organizations and the public.

  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. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep.

    PubMed

    Heijs, Sander K; Haese, Ralf R; van der Wielen, Paul W J J; Forney, Larry J; van Elsas, Jan Dirk

    2007-04-01

    This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22-34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0-6 cm). Communities in the middle layer (6-22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study.

  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. Revised Extended Grid Library

    SciTech Connect

    Martz, Roger L.

    2016-07-15

    The Revised Eolus Grid Library (REGL) is a mesh-tracking library that was developed for use with the MCNP6TM computer code so that (radiation) particles can track on an unstructured mesh. The unstructured mesh is a finite element representation of any geometric solid model created with a state-of-the-art CAE/CAD tool. The mesh-tracking library is written using modern Fortran and programming standards; the library is Fortran 2003 compliant. The library was created with a defined application programmer interface (API) so that it could easily integrate with other particle tracking/transport codes. The library does not handle parallel processing via the message passing interface (mpi), but has been used successfully where the host code handles the mpi calls. The library is thread-safe and supports the OpenMP paradigm. As a library, all features are available through the API and overall a tight coupling between it and the host code is required. Features of the library are summarized with the following list: • can accommodate first and second order 4, 5, and 6-sided polyhedra • any combination of element types may appear in a single geometry model • parts may not contain tetrahedra mixed with other element types • pentahedra and hexahedra can be together in the same part • robust handling of overlaps and gaps • tracks element-to-element to produce path length results at the element level • finds element numbers for a given mesh location • finds intersection points on element faces for the particle tracks • produce a data file for post processing results analysis • reads Abaqus .inp input (ASCII) files to obtain information for the global mesh-model • supports parallel input processing via mpi • support parallel particle transport by both mpi and OpenMP

  18. 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.

  19. 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)…

  20. 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…

  1. 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…

  2. Brown County Library: Library of the Year 1994.

    ERIC Educational Resources Information Center

    Berry, John

    1994-01-01

    Describes the management, programs, and services at the Brown County Library (Wisconsin), winner of the Library of the Year award sponsored by Gale Research Inc, and "Library Journal." Highlights include involvement of library staff; financial support; total quality management; coalitions with local businesses, community agencies, and…

  3. Redwood City Public Library: Library of the Year 1992.

    ERIC Educational Resources Information Center

    Berry, John

    1992-01-01

    Describes programs at the Redwood City Public Library (California), winner of the Library of the Year Award from Gale Research Inc. and "Library Journal." Highlights include a newly renovated building; a mission statement that reflects the library's role; staff development; increases in circulation and reference; children's services; and…

  4. 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…

  5. 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…

  6. IFLA General Conference, 1989. Division of General Research Libraries. Section of National Libraries; Section of University Libraries and Other General Research Libraries; Section of Parliamentary Libraries. Booklet 10.

    ERIC Educational Resources Information Center

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

    There are 11 papers from the Division of General Research Libraries in this compilation: (1) "National Library and Information Needs: Alternative Ways of Meeting Them, with Special Reference to the Role of National Libraries" (Maurice B. Line); (2) "Managing Change in National LIbraries: The Library of Congress" (James H.…

  7. Library - Book Trade Relations

    ERIC Educational Resources Information Center

    Tuttle, Helen Welch

    1970-01-01

    The trend in relations between the library and the book trade has been in the direction of increased communication and cooperation. Organizational links between librarians, publishers, and booksellers are discussed. (Author/JS)

  8. 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)

  9. Controlling hospital library theft.

    PubMed

    Cuddy, Theresa M; Marchok, Catherine

    2003-04-01

    At Capital Health System/Fuld Campus (formerly Helene Fuld Medical Center), the Health Sciences Library lost many books and videocassettes. These materials were listed in the catalog but were missing when staff went to the shelves. The hospital had experienced a downsizing of staff, a reorganization, and a merger. When the library staff did an inventory, $10,000 worth of materials were found to be missing. We corrected the situation through a series of steps that we believe will help other libraries control their theft. Through regularly scheduling inventories, monitoring items, advertising, and using specific security measures, we have successfully controlled the library theft. The January 2002 inventory resulted in meeting our goal of zero missing books and videocassettes. We work to maintain that goal.

  10. 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)

  11. 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)

  12. Directions in Library Networking.

    ERIC Educational Resources Information Center

    Avram, Henriette D.; McCallum, Sally H.

    1980-01-01

    Reviews bibliographic control before and after the advent of machine-readable cataloging, and holds that new developments toward decentralization seem to counter the existing technological trend toward centralization of automated library services. (FM)

  13. Controlling hospital library theft

    PubMed Central

    Cuddy, Theresa M.; Marchok, Catherine

    2003-01-01

    At Capital Health System/Fuld Campus (formerly Helene Fuld Medical Center), the Health Sciences Library lost many books and videocassettes. These materials were listed in the catalog but were missing when staff went to the shelves. The hospital had experienced a downsizing of staff, a reorganization, and a merger. When the library staff did an inventory, $10,000 worth of materials were found to be missing. We corrected the situation through a series of steps that we believe will help other libraries control their theft. Through regularly scheduling inventories, monitoring items, advertising, and using specific security measures, we have successfully controlled the library theft. The January 2002 inventory resulted in meeting our goal of zero missing books and videocassettes. We work to maintain that goal. PMID:12883573

  14. Fact Book on Library Aid.

    ERIC Educational Resources Information Center

    New York State Education Dept., Albany. Div. of Library Development.

    This booklet presents information about the financial support authorized for libraries and library systems in Chapter 917 of the "Laws of 1990" and advocated by the Regents of the State University of New York for the state's library systems. It is noted that, although Chapter 917 provides for modest increases in library aid each year for…

  15. Canadian Literature in American Libraries

    ERIC Educational Resources Information Center

    Rogers, A. Robert

    1973-01-01

    Acquisition of Canadian literature by American libraries was investigated in three ways: questionnaires were sent to selected large libraries, titles were checked against the National Union Catalog'' and published literature describing major collections was examined. With the exception of the Library of Congress, American libraries purchase…

  16. 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…

  17. Directory of Academic Library Consortia.

    ERIC Educational Resources Information Center

    Delanoy, Diana D.; Caudra, Carlos, A.

    The purpose of this directory is to identify and describe all academic library consortia in the continental United States that satisfy the following specified criteria for inclusion: participating institutions must be autonomous, more than half the members must be academic libraries, two or more libraries must be involved, library consortia must…

  18. 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…

  19. 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…

  20. 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.…

  1. Quality Library Services, K-12.

    ERIC Educational Resources Information Center

    Ohio State Dept. of Education, Columbus.

    Developed to promote excellence in Ohio's school libraries, this document is designed to: (1) provide a rationale for integration of the school library into the total education program; (2) delineate the dimensions of service of a dynamic K-12 library program; (3) identify essential components of an effective K-12 library program; (4) provide a…

  2. Public Libraries: Responding to Demand.

    ERIC Educational Resources Information Center

    Annichiarico, Mark; And Others

    1993-01-01

    Discussion of problems library wholesalers/distributors face trying to fulfill public libraries' needs while adjusting to a changing industry is based on responses by librarians to a survey on library jobbers. Increased services to libraries, electronic ordering, timeliness, stock management, and quality control are addressed; and a chart of…

  3. Vermont: Library and Information Technology.

    ERIC Educational Resources Information Center

    Klinck, Patricia E.

    1996-01-01

    Describes the Vermont Automated Libraries System and the use of information technology. Topics include rural public library access; software; multitype library cooperation, including public, school, academic, and special libraries; Internet access; government information; public user access; system design; document delivery capabilities; and…

  4. The Economics of Library Innovation.

    ERIC Educational Resources Information Center

    Drake, Miriam A.; Olsen, Harold A.

    1979-01-01

    Presents a review of the economic literature dealing with innovation in academic libraries, and of the economic environment and structure of libraries and their relationship to innovation. Also discussed are sources of capital for libraries, the economic character of innovation, and innovation in libraries. (Author/MBR)

  5. 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…

  6. A Library of Infectious Hepatitis C Viruses with Engineered Mutations in the E2 Gene Reveals Growth-Adaptive Mutations That Modulate Interactions with Scavenger Receptor Class B Type I.

    PubMed

    Zuiani, Adam; Chen, Kevin; Schwarz, Megan C; White, James P; Luca, Vincent C; Fremont, Daved H; Wang, David; Evans, Matthew J; Diamond, Michael S

    2016-12-01

    While natural hepatitis C virus (HCV) infection results in highly diverse quasispecies of related viruses over time, mutations accumulate more slowly in tissue culture, in part because of the inefficiency of replication in cells. To create a highly diverse population of HCV particles in cell culture and identify novel growth-enhancing mutations, we engineered a library of infectious HCV with all codons represented at most positions in the ectodomain of the E2 gene. We identified many putative growth-adaptive mutations and selected nine highly represented E2 mutants for further study: Q412R, T416R, S449P, T563V, A579R, L619T, V626S, K632T, and L644I. We evaluated these mutants for changes in particle-to-infectious-unit ratio, sensitivity to neutralizing antibody or CD81 large extracellular loop (CD81-LEL) inhibition, entry factor usage, and buoyant density profiles. Q412R, T416R, S449P, T563V, and L619T were neutralized more efficiently by anti-E2 antibodies and T416R, T563V, and L619T by CD81-LEL. Remarkably, all nine variants showed reduced dependence on scavenger receptor class B type I (SR-BI) for infection. This shift from SR-BI usage did not correlate with a change in the buoyant density profiles of the variants, suggesting an altered E2-SR-BI interaction rather than changes in the virus-associated lipoprotein-E2 interaction. Our results demonstrate that residues influencing SR-BI usage are distributed across E2 and support the development of large-scale mutagenesis studies to identify viral variants with unique functional properties.

  7. Library Code Security Analysis

    DTIC Science & Technology

    2013-11-01

    to identify previously unknown vulnerabilities in Java libraries. This technology will give previously unavailable insight into the security posture...researchers from Aspect Security have created a new approach to analyzing third party Java libraries for vulnerabilities and potential hazards. This...report documents the challenges in this endeavor, the tasks performed to create such a tool, and the results from analyzing thirty of the most common

  8. 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.

  9. 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.

  10. Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.

    PubMed

    Danhorn, Thomas; Young, Curtis R; DeLong, Edward F

    2012-11-01

    The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries suggested that this was caused by a relative underrepresentation of dominant taxonomic groups with low GC content, notably Prochlorales and the SAR11 cluster, in fosmid libraries. While these abundant taxa had a large impact on library representation, we also observed a positive correlation between taxon GC content and fosmid library representation in other low-GC taxa, suggesting a general trend. Analysis of gene category representation in different libraries indicated that the functional composition of a library was largely a reflection of its taxonomic composition, and no additional systematic biases against particular functional categories were detected at the level of sequencing depth in our samples. Another important but less predictable factor influencing the apparent taxonomic and functional library composition was the read length afforded by the different sequencing technologies. Our comparisons and analyses provide a detailed perspective on the influence of library type on the recovery of microbial taxa in metagenomic libraries and underscore the different uses and utilities of more traditional, as well as contemporary 'next-generation' DNA library construction and sequencing technologies for exploring the genomics of the natural microbial world.

  11. 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

  12. Human chromosome-specific DNA libraries: construction and availability

    SciTech Connect

    Van Dilla, M.A.; Deaven, L.L.; Albright, K.L.; Allen, N.A.; Aubuchon, M.R.; Bartholdi, M.F.; Brown, N.C.; Campbell, E.W.; Carrano, A.V.; Clark, L.M.; Cram, L.S.

    1986-06-01

    The goal of the National Laboratory Gene Library Project at the Los Alamos and Lawrence Livermore National Laboratories is the production of chromosome-specific human gene libraries and their distribution to the scientific community for studies of the molecular biology of genes and chromosomes, and for the study and diagnosis of genetic disease. The specific aim of Phase I of the project is the production of complete digest (4 kb average insert size) libraries from each of the 24 human chromosomal types purified by flow sorting. The bacteriophage vector is Charon 21A, which has both Eco R1 and Hind III insertion sites accommodating human DNA fragments up to 9.1 kb in size. Each laboratory has undertaken production of a complete set of chromosome-specific libraries, Los Alamos with Eco R1 and Livermore with Hind III; most of this task has now been accomplished. Close to 1200 library aliquots have been sent to about 300 laboratories world-wide through February 1986, at which time repository and distribution functions were transferred to the American Type Culture Collection, Rockville, MD. Following Phase I, libraries will be constructed with large inserts in a more advanced, recently developed bacteriophage vector (about 20 kb inserts) or in a cosmid vector (about 40 kb inserts), and with characteristics better suited to basic studies of gene structure and function.

  13. Directed evolution of nucleotide-based libraries using lambda exonuclease.

    PubMed

    Lim, Bee Nar; Choong, Yee Siew; Ismail, Asma; Glökler, Jörn; Konthur, Zoltán; Lim, Theam Soon

    2012-12-01

    Directed evolution of nucleotide libraries using recombination or mutagenesis is an important technique for customizing catalytic or biophysical traits of proteins. Conventional directed evolution methods, however, suffer from cumbersome digestion and ligation steps. Here, we describe a simple method to increase nucleotide diversity using single-stranded DNA (ssDNA) as a starting template. An initial PCR amplification using phosphorylated primers with overlapping regions followed by treatment with lambda exonuclease generates ssDNA templates that can then be annealed via the overlap regions. Double-stranded DNA (dsDNA) is then generated through extension with Klenow fragment. To demonstrate the applicability of this methodology for directed evolution of nucleotide libraries, we generated both gene shuffled and regional mutagenesis synthetic antibody libraries with titers of 2×108 and 6×107, respectively. We conclude that our method is an efficient and convenient approach to generate diversity in nucleic acid based libraries, especially recombinant antibody libraries.

  14. Las Campanas Stellar Library

    NASA Astrophysics Data System (ADS)

    Chilingarian, Igor; Zolotukhin, Ivan; Beletsky, Yuri; Worthey, Guy

    2015-08-01

    Stellar libraries are fundamental tools required to understand stellar populations in star clusters and galaxies as well as properties of individual stars. Comprehensive libraries exist in the optical domain, but the near-infrared (NIR) domain stays a couple of decades behind. Here we present the Las Campanas Stellar Library project aiming at obtaining high signal-to-noise intermediate-resolution (R=8000) NIR spectra (0.83<λ<2.5μm) for a sample of 1200 stars in the Southern sky using the Folded-port InfraRed Echelette spectrograph at the 6.5-m Magellan Baade telescope. We developed a dedicated observing strategy and customized the telescope control software in order to achieve the highest possible level of data homogeniety. As of 2015, we observed about 600 stars of all spectral types and luminosity classes making our library the largest homogeneous collection of stellar spectra covering the entire NIR domain. We also re-calibrated in flux and wavelength the two existing optical stellar libraries, INDO-US and UVES-POP and followed up about 400 non-variable stars in the NIR in order to get complete optical-NIR coverage. Worth mentioning that our current sample includes about 80 AGB stars and a few dozens of bulge/LMC/SMC stars.

  15. Polyelemental nanoparticle libraries

    NASA Astrophysics Data System (ADS)

    Chen, Peng-Cheng; Liu, Xiaolong; Hedrick, James L.; Xie, Zhuang; Wang, Shunzhi; Lin, Qing-Yuan; Hersam, Mark C.; Dravid, Vinayak P.; Mirkin, Chad A.

    2016-06-01

    Multimetallic nanoparticles are useful in many fields, yet there are no effective strategies for synthesizing libraries of such structures, in which architectures can be explored in a systematic and site-specific manner. The absence of these capabilities precludes the possibility of comprehensively exploring such systems. We present systematic studies of individual polyelemental particle systems, in which composition and size can be independently controlled and structure formation (alloy versus phase-separated state) can be understood. We made libraries consisting of every combination of five metallic elements (Au, Ag, Co, Cu, and Ni) through polymer nanoreactor-mediated synthesis. Important insight into the factors that lead to alloy formation and phase segregation at the nanoscale were obtained, and routes to libraries of nanostructures that cannot be made by conventional methods were developed.

  16. DOLIB: Distributed Object Library

    SciTech Connect

    D`Azevedo, E.F.; Romine, C.H.

    1994-10-01

    This report describes the use and implementation of DOLIB (Distributed Object Library), a library of routines that emulates global or virtual shared memory on Intel multiprocessor systems. Access to a distributed global array is through explicit calls to gather and scatter. Advantages of using DOLIB include: dynamic allocation and freeing of huge (gigabyte) distributed arrays, both C and FORTRAN callable interfaces, and the ability to mix shared-memory and message-passing programming models for ease of use and optimal performance. DOLIB is independent of language and compiler extensions and requires no special operating system support. DOLIB also supports automatic caching of read-only data for high performance. The virtual shared memory support provided in DOLIB is well suited for implementing Lagrangian particle tracking techniques. We have also used DOLIB to create DONIO (Distributed Object Network I/O Library), which obtains over a 10-fold improvement in disk I/O performance on the Intel Paragon.

  17. XAFS Model Compound Library

    DOE Data Explorer

    Newville, Matthew

    The XAFS Model Compound Library contains XAFS data on model compounds. The term "model" compounds refers to compounds of homogeneous and well-known crystallographic or molecular structure. Each data file in this library has an associated atoms.inp file that can be converted to a feff.inp file using the program ATOMS. (See the related Searchable Atoms.inp Archive at http://cars9.uchicago.edu/~newville/adb/) This Library exists because XAFS data on model compounds is useful for several reasons, including comparing to unknown data for "fingerprinting" and testing calculations and analysis methods. The collection here is currently limited, but is growing. The focus to date has been on inorganic compounds and minerals of interest to the geochemical community. [Copied, with editing, from http://cars9.uchicago.edu/~newville/ModelLib/

  18. MTV Utility Library

    SciTech Connect

    Lurie, Gordon; Taxon, Thomas; Kehrer, Michelle; Simunich, Kathy Lee

    2008-02-29

    The MSV Java Utility Library contains software developed over many years for many sponsors. (This work is not a derivative of CB-EMIS), but rather support to the CB-EMIS software). Projects that have used and contributed to code in this library: CB-EMIS (PROTECT), BWIC, Fort Future, Teva, Integrated Oceans, ENKIMDU, RCW, JEMS, JWACS, EPA watershed, and many others. This library will continue to be used in other non-CB-EMIS related projects. The components include: Spatial components: Multi-coordinate system spatial objects. 2D spatial indexing system, and polygon griding system. Data translation: Allows import and export of file based data to and from object oriented systems. Multi-platform data streams: Allows platform specific data streams to operate on any support platform. Other items include printing, custom GUI components, support for NIMA Raster Product Format, program logging utilities and others.

  19. Secure medical digital libraries.

    PubMed

    Papadakis, I; Chrissikopoulos, V; Polemi, D

    2001-12-01

    In this paper, a secure medical digital library is presented. It is based on the CORBA specifications for distributed systems. The described approach relies on a three-tier architecture. Interaction between the medical digital library and its users is achieved through a Web server. The choice of employing Web technology for the dissemination of medical data has many advantages compared to older approaches, but also poses extra requirements that need to be fulfilled. Thus, special attention is paid to the distinguished nature of such medical data, whose integrity and confidentiality should be preserved at all costs. This is achieved through the employment of Trusted Third Parties (TTP) technology for the support of the required security services. Additionally, the proposed digital library employs smartcards for the management of the various security tokens that are used from the above services.

  20. The Automatic Library Tracking Database

    SciTech Connect

    Fahey, Mark R; Jones, Nicholas A; Hadri, Bilel

    2010-01-01

    A library tracking database has been developed and put into production at the National Institute for Computational Sciences and the Oak Ridge Leadership Computing Facility (both located at Oak Ridge National Laboratory.) The purpose of the library tracking database is to track which libraries are used at link time on Cray XT5 Supercomputers. The database stores the libraries used at link time and also records the executables run in a batch job. With this data, many operationally important questions can be answered such as which libraries are most frequently used and which users are using deprecated libraries or applications. The infrastructure design and reporting mechanisms are presented along with collected production data.

  1. Library resources on the Internet

    NASA Astrophysics Data System (ADS)

    Buchanan, Nancy L.

    1995-07-01

    Library resources are prevalent on the Internet. Library catalogs, electronic books, electronic periodicals, periodical indexes, reference sources, and U.S. Government documents are available by telnet, Gopher, World Wide Web, and FTP. Comparatively few copyrighted library resources are available freely on the Internet. Internet implementations of library resources can add useful features, such as full-text searching. There are discussion lists, Gophers, and World Wide Web pages to help users keep up with new resources and changes to existing ones. The future will bring more library resources, more types of library resources, and more integrated implementations of such resources to the Internet.

  2. Library construction and evaluation for site saturation mutagenesis.

    PubMed

    Sullivan, Bradford; Walton, Adam Z; Stewart, Jon D

    2013-06-10

    We developed a method for creating and evaluating site-saturation libraries that consistently yields an average of 27.4±3.0 codons of the 32 possible within a pool of 95 transformants. This was verified by sequencing 95 members from 11 independent libraries within the gene encoding alkene reductase OYE 2.6 from Pichia stipitis. Correct PCR primer design as well as a variety of factors that increase transformation efficiency were critical contributors to the method's overall success. We also developed a quantitative analysis of library quality (Q-values) that defines library degeneracy. Q-values can be calculated from standard fluorescence sequencing data (capillary electropherograms) and the degeneracy predicted from an early stage of library construction (pooled plasmids from the initial transformation) closely matched that observed after ca. 1000 library members were sequenced. Based on this experience, we suggest that this analysis can be a useful guide when applying our optimized protocol to new systems, allowing one to focus only on good-quality libraries and reject substandard libraries at an early stage. This advantage is particularly important when lower-throughput screening techniques such as chiral-phase GC must be employed to identify protein variants with desirable properties, e.g., altered stereoselectivities or when multiple codons are targeted for simultaneous randomization.

  3. Interior view, law library (formerly Old Patent Office Library) ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior view, law library (formerly Old Patent Office Library) - United States Department of Commerce, Bounded by Fourteenth, Fifteenth, and E streets and Constitution Avenue, Washington, District of Columbia, DC

  4. Application Portable Parallel Library

    NASA Technical Reports Server (NTRS)

    Cole, Gary L.; Blech, Richard A.; Quealy, Angela; Townsend, Scott

    1995-01-01

    Application Portable Parallel Library (APPL) computer program is subroutine-based message-passing software library intended to provide consistent interface to variety of multiprocessor computers on market today. Minimizes effort needed to move application program from one computer to another. User develops application program once and then easily moves application program from parallel computer on which created to another parallel computer. ("Parallel computer" also include heterogeneous collection of networked computers). Written in C language with one FORTRAN 77 subroutine for UNIX-based computers and callable from application programs written in C language or FORTRAN 77.

  5. PANEL LIBRARY AND EDITOR

    NASA Technical Reports Server (NTRS)

    Raible, E.

    1994-01-01

    The Panel Library and Editor is a graphical user interface (GUI) builder for the Silicon Graphics IRIS workstation family. The toolkit creates "widgets" which can be manipulated by the user. Its appearance is similar to that of the X-Windows System. The Panel Library is written in C and is used by programmers writing user-friendly mouse-driven applications for the IRIS. GUIs built using the Panel Library consist of "actuators" and "panels." Actuators are buttons, dials, sliders, or other mouse-driven symbols. Panels are groups of actuators that occupy separate windows on the IRIS workstation. The application user can alter variables in the graphics program, or fire off functions with a click on a button. The evolution of data values can be tracked with meters and strip charts, and dialog boxes with text processing can be built. Panels can be stored as icons when not in use. The Panel Editor is a program used to interactively create and test panel library interfaces in a simple and efficient way. The Panel Editor itself uses a panel library interface, so all actions are mouse driven. Extensive context-sensitive on-line help is provided. Programmers can graphically create and test the user interface without writing a single line of code. Once an interface is judged satisfactory, the Panel Editor will dump it out as a file of C code that can be used in an application. The Panel Library (v9.8) and Editor (v1.1) are written in C-Language (63%) and Scheme, a dialect of LISP, (37%) for Silicon Graphics 4D series workstations running IRIX 3.2 or higher. Approximately 10Mb of disk space is required once compiled. 1.5Mb of main memory is required to execute the panel editor. This program is available on a .25 inch streaming magnetic tape cartridge in UNIX tar format for an IRIS, and includes a copy of XScheme, the public-domain Scheme interpreter used by the Panel Editor. The Panel Library Programmer's Manual is included on the distribution media. The Panel Library and

  6. DOLIB: Distributed object library

    SciTech Connect

    D`Azevedo, E.F.; Romine, C.H.

    1995-12-01

    DOLIB (Distributed Object Library) emulates global shared memory in distributed memory environments intended for scientific applications. Access to global arrays is through explicit calls to gather and scatter. Use of DOLIB does not rely on language extension, compiler or operating system supports. Shared memory provided by DOLIB was also used by DONIO (Distributed Network I/O Library) as large disk caches that gave improvements of 15 to 30 fold on the Intel Paragon. DOLIB shared memory simplifies the parallelization of the CHAMMP Semi-Lagrangian Transport (SLT) code that has particle tracking as the kernel computation.

  7. Enterprise Reference Library

    NASA Technical Reports Server (NTRS)

    Bickham, Grandin; Saile, Lynn; Havelka, Jacque; Fitts, Mary

    2011-01-01

    Introduction: Johnson Space Center (JSC) offers two extensive libraries that contain journals, research literature and electronic resources. Searching capabilities are available to those individuals residing onsite or through a librarian s search. Many individuals have rich collections of references, but no mechanisms to share reference libraries across researchers, projects, or directorates exist. Likewise, information regarding which references are provided to which individuals is not available, resulting in duplicate requests, redundant labor costs and associated copying fees. In addition, this tends to limit collaboration between colleagues and promotes the establishment of individual, unshared silos of information The Integrated Medical Model (IMM) team has utilized a centralized reference management tool during the development, test, and operational phases of this project. The Enterprise Reference Library project expands the capabilities developed for IMM to address the above issues and enhance collaboration across JSC. Method: After significant market analysis for a multi-user reference management tool, no available commercial tool was found to meet this need, so a software program was built around a commercial tool, Reference Manager 12 by The Thomson Corporation. A use case approach guided the requirements development phase. The premise of the design is that individuals use their own reference management software and export to SharePoint when their library is incorporated into the Enterprise Reference Library. This results in a searchable user-specific library application. An accompanying share folder will warehouse the electronic full-text articles, which allows the global user community to access full -text articles. Discussion: An enterprise reference library solution can provide a multidisciplinary collection of full text articles. This approach improves efficiency in obtaining and storing reference material while greatly reducing labor, purchasing and

  8. Chromosome region-specific libraries for human genome analysis

    SciTech Connect

    Kao, Fa-Ten.

    1992-08-01

    During the grant period progress has been made in the successful demonstration of regional mapping of microclones derived from microdissection libraries; successful demonstration of the feasibility of converting microclones with short inserts into yeast artificial chromosome clones with very large inserts for high resolution physical mapping of the dissected region; Successful demonstration of the usefulness of region-specific microclones to isolate region-specific cDNA clones as candidate genes to facilitate search for the crucial genes underlying genetic diseases assigned to the dissected region; and the successful construction of four region-specific microdissection libraries for human chromosome 2, including 2q35-q37, 2q33-q35, 2p23-p25 and 2p2l-p23. The 2q35-q37 library has been characterized in detail. The characterization of the other three libraries is in progress. These region-specific microdissection libraries and the unique sequence microclones derived from the libraries will be valuable resources for investigators engaged in high resolution physical mapping and isolation of disease-related genes residing in these chromosomal regions.

  9. Rhode Island: Multi-library Networks and the Virtual Library.

    ERIC Educational Resources Information Center

    Weaver, Barbara; And Others

    1996-01-01

    Describes the multilibrary network in Rhode Island which provides electronic access to public information. Highlights include the role of the Department of State Library Services; Internet access issues; a network for elementary and secondary schools that provides access to university and public libraries; a higher education library network; a…

  10. Applying DEA Technique to Library Evaluation in Academic Research Libraries.

    ERIC Educational Resources Information Center

    Shim, Wonsik

    2003-01-01

    This study applied an analytical technique called Data Envelopment Analysis (DEA) to calculate the relative technical efficiency of 95 academic research libraries, all members of the Association of Research Libraries. DEA, with the proper model of library inputs and outputs, can reveal best practices in the peer groups, as well as the technical…

  11. Montana Library Laws, Rules, and Public Library Standards.

    ERIC Educational Resources Information Center

    Montana State Library, Helena.

    Chapter 1 of this handbook of Montana library laws, rules, and public library standards contains excerpts from the Constitution of Montana, including articles on property tax exemptions, educational goals and duties, and code of ethics. Montana library laws covering the following areas are presented in Chapter 2: publication and updating of the…

  12. Geography and Map Libraries Section. Special Libraries Division. Papers.

    ERIC Educational Resources Information Center

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

    Papers on geography and map libraries and a paper on European access to biomedical databases, which were presented at the 1983 International Federation of Library Associations (IFLA) conference, include: (1) "History and Current Status of the Globe Museum of the Austrian National Library" by Franz Wawrik (Austria); (2) "Earth…

  13. Science and Technology Libraries Section. Special Libraries Division. Papers.

    ERIC Educational Resources Information Center

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

    Papers on scientific/technical information and libraries, which were presented at the 1983 International Federation of Library Associations (IFLA) conference, include: (1) "Patents as Information--An Unused Resource" by Richard D. Walker (United States); (2) "Survey of the Information Services of the Library of the German Patent…

  14. Public Libraries Section. Libraries Serving the General Public Division. Papers.

    ERIC Educational Resources Information Center

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

    Papers on the impact of information technology on library services and the provision of library services to ethnic and linguistic minorities which were presented at the 1982 International Federation of Library Associations (IFLA) conference include: (1) "The Challenge of Electronic Technologies to the Information Society: A Call for…

  15. Law Libraries as Special Libraries: An Educational Model.

    ERIC Educational Resources Information Center

    Hazelton, Penny A.

    1993-01-01

    Summarizes the history of the law library profession and the development of the educational model for law librarians in light of the particular demands and needs of corporate and law firm libraries. Guidelines of the American Association of Law Libraries for graduate programs in law librarianship are discussed. (Contains 17 references.) (LRW)

  16. Is Your Academic Library Pinning? Academic Libraries and Pinterest

    ERIC Educational Resources Information Center

    Thornton, Elaine

    2012-01-01

    Academic libraries are flocking to online social networking sites in an effort to meet users where they are. Pinterest is the latest of these rapidly growing online social networking tools. The author of this article reports results from a survey on academic libraries' presence on Pinterest. The survey found most academic library pinboards are in…

  17. Library of the Future: Croydon's New Central Library Complex.

    ERIC Educational Resources Information Center

    Batt, Chris

    1993-01-01

    A new library and cultural center in Croyden (England) is described. Function-based areas include library, administration, technical services, museum and galleries, museum offices and store, cinema, tourist information center, and local government offices. Information technology systems include the library management system, office automation, and…

  18. Children's Libraries Section. Libraries Serving the General Public Division. Papers.

    ERIC Educational Resources Information Center

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

    Papers on school and children's libraries which were presented at the 1982 International Federation of Library Associations (IFLA) conference include: (1) "Learning to Learn in the Street," a description by B. Lang (France) of "street libraries" and other institutions designed to introduce economically disadvantaged children to…

  19. This I Believe...All Libraries Should Be Teaching Libraries

    ERIC Educational Resources Information Center

    Palmer, Catherine

    2011-01-01

    In this article, I imagine a library that prioritizes teaching users how to find, evaluate, and use information over the traditional library public service activities of collection development, access to materials, and reference services. If I ran the library, all services would support end-user education. (Contains 1 graph and 1 note.)

  20. Medina County District Library: 1998 Library of the Year.

    ERIC Educational Resources Information Center

    Berry, John

    1998-01-01

    Describes services offered and problems encountered at the Medina County (Ohio) District Library, winner of the Gale Research/Library Journal Library of the Year Award. Highlights include resisting pressure from the religious right to limit children's Internet access to protect them from pornography; a successful tax levy; and growth in…

  1. Regional Libraries and the Depository Library Act of 1962.

    ERIC Educational Resources Information Center

    Schwarzkopf, LeRoy C.

    This report is a ten year review of the regional depository library system for federal government documents which was established by the Depository Library Act of 1962. It describes the status of programs which regional libraries have undertaken to comply with the requirements of the Act to "provide interlibrary loan, reference service, and…

  2. It's Cool to Work in the Library... Student Library Aides

    ERIC Educational Resources Information Center

    Schipman, Mavis

    2006-01-01

    The Student Library Aide Program provides real-world work experience to students in a safe learning environment. Students who are interested in working in the library complete an application form similar to a real job application listing their classroom teachers as references, telling why they want to work in the library, and any experience they…

  3. Library Buildings 2004: Great Libraries in the Making

    ERIC Educational Resources Information Center

    Martin, Elisabeth; Kenney, Brian

    2004-01-01

    In an age of experimentation, library users from Cerritos, California, to Salt Lake City to Seattle are experiencing public libraries the likes of which they have never before seen. While the 1990s may be remembered as the era of the anchor facility, when libraries were called upon to define and support a community's renaissance, this decade's…

  4. National Libraries Section. General Research Libraries Division. Papers.

    ERIC Educational Resources Information Center

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

    Papers on national networks and national libraries and information centers presented at the 1982 International Federation of Library Associations (IFLA) conference include: (1) "Networking Developments in the U.S. at the National Level," in which Warren J. Haas predicts the development of links between existing library bibliographic…

  5. "Old Library." Photo no. 567. South front, library, looking northeast ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    "Old Library." Photo no. 567. South front, library, looking northeast across the lawn. Original print is a 5x7" enlargement from a 35mm negative. No other marks. - San Bernardino Valley College, Library, 701 South Mount Vernon Avenue, San Bernardino, San Bernardino County, CA

  6. Library Materials Cost Studies in ARL Libraries. SPEC Kit 95.

    ERIC Educational Resources Information Center

    Lynden, Frederick C.

    Replacing a January 1980 publication of the same title, this collection of cost tables and other documentation from library materials cost studies conducted by members of the Association of Research Libraries (ARL) or by library vendors contains excerpts from: (1) local cost studies conducted at Colorado State University, Indiana University, Iowa…

  7. Public Libraries: On the Skids?

    ERIC Educational Resources Information Center

    Eisner, Joseph

    1971-01-01

    It does not appear that there will be significant improvements in library funding for the foreseeable future. Public libraries will have to adjust their services and programs to the reality imposed by fiscal constraints. (10 references) (Author)

  8. Toward the Library-Bookstore

    ERIC Educational Resources Information Center

    Severtson, Susan; Banks, George

    1971-01-01

    Close collaboration between library and bookstore (or a complete merger of the two) could do much to solve the immediate problems faced by many small colleges with small library collections and limited budgets. (MF)

  9. Public Libraries: Adapting to Change.

    ERIC Educational Resources Information Center

    Durrance, Joan; Van Fleet, Connie

    1992-01-01

    Reports on a study of changing trends in public libraries. Interviews with public library leaders identified five areas of changing emphasis: information technology, community needs, strategic planning, public relations and marketing, and funding. (seven references) (EA)

  10. Scavenging for Better Library Instruction.

    ERIC Educational Resources Information Center

    Cocking, Terry S.; Schafer, Susan A.

    1994-01-01

    Describes the Library Scavenger Hunt program at Baylor University (part of the reading and study skills program) which emphasizes learning what sources are available in a college library, where they are located, and how to use them. (SR)

  11. The Shoestring Library

    ERIC Educational Resources Information Center

    Fullner, Sheryl Kindle

    2010-01-01

    An organized collection of budget saving methods, materials, and strategies, these tips are all tried-and-true examples of ways to stretch the media specialist's budget and time, and change even the drabbest library into an inviting oasis of learning. Makeovers are mesmerizing. Whether it is the 400-pound man who turns into a hunk or a hovel that…

  12. Alleviating Library Anxiety

    ERIC Educational Resources Information Center

    Nicol, Erica Carlson

    2009-01-01

    As librarians work to make their services more user-centered, to put forward their best and most approachable faces in order to meet user needs, they are still met with students who approach them hesitantly and apologize for asking them questions, and by students who are obviously intimidated by the libraries in which they work. A good part of…

  13. Energy Efficiency in Libraries.

    ERIC Educational Resources Information Center

    Lewis, Eleanor J.; And Others

    1993-01-01

    Shows how libraries can save money and energy with energy-efficient technologies, improving maintenance, and encouraging staff efforts to conserve energy. Specific techniques such as life-cycle cost analysis and energy audits focusing on lighting, heating, ventilation, air conditioning, and water efficiency are described. Funding options and…

  14. Libraries, Learning and Fun

    ERIC Educational Resources Information Center

    Coatney, Sharon

    2004-01-01

    Learning can be packaged and promoted as fun. The youngest learners naturally perceive all of life as one big wonder. It is important for school libraries to be the catalyst in helping to position learning as being the "fun" part of school. Sometimes, the simplest learning activity, embellished and celebrated can become a very meaningful…

  15. Automating Small Libraries.

    ERIC Educational Resources Information Center

    Swan, James

    1996-01-01

    Presents a four-phase plan for small libraries strategizing for automation: inventory and weeding, data conversion, implementation, and enhancements. Other topics include selecting a system, MARC records, compatibility, ease of use, industry standards, searching capabilities, support services, system security, screen displays, circulation modules,…

  16. Libraries and Automation.

    ERIC Educational Resources Information Center

    Markuson, Barbara Evans, Ed.

    The arrangement of this publication follows, as nearly as possible, the actual conference program. The seven sections represent the topics selected by the planning committee as areas of concentration. Each section includes a state-of-the-art paper and related talks and discussion. The topics covered are: the library of the future, file…

  17. Not Your Grandmother's Library!

    ERIC Educational Resources Information Center

    Perez, Lisa

    2011-01-01

    School libraries are an essential part of a complete school program. They provide an equitable, fiscally responsible strategy for sharing resources across grade levels and the curriculum while addressing core reading, information, and technology literacies. Students are still voracious readers of books in print, and now they consume a variety of…

  18. Virtual Libraries: Service Realities.

    ERIC Educational Resources Information Center

    Novak, Jan

    This paper discusses client service issues to be considered when transitioning to a virtual library situation. Themes related to the transitional nature of society in the knowledge era are presented, including: paradox and a contradictory nature; blurring of boundaries; networks, systems, and holistic thinking; process/not product, becoming/not…

  19. Success in Library School.

    ERIC Educational Resources Information Center

    Magrill, Rose Mary; Rinehart, Constance

    1979-01-01

    Data on admission characteristics and performance in library school were collected for students entering the A.M.L.S. program at the University of Michigan. Success measures--completion of degree, G.P.A., and amount of time required to complete degree--showed little relation to admission variables in determining success. (Author/MBR)

  20. Shaping Digital Library Content.

    ERIC Educational Resources Information Center

    Miller, Rush G.

    2002-01-01

    Explores issues related to the selection and purchase of digital content in academic libraries, including commercially-produced databases, electronic journals, and books and other electronic resources that are purchased from vendors; and in-house digitization projects. Considers the degree to which standard collection management principles apply.…

  1. My Infinite Library.

    ERIC Educational Resources Information Center

    Gould, Warwick

    2002-01-01

    A literary scholar interacts with various other speakers at the Fleur Cowles "Fleur" Symposium 2000 (Austin, TX) and makes his own case for the necessity of physical materials that are always yielding new insights. He rues the apparent denigration of paper materials and the reduction of books even in research libraries and suggests that research…

  2. Young Adult Library Services.

    ERIC Educational Resources Information Center

    The Bookmark, 1985

    1985-01-01

    Eight articles in this Spring 1985 issue of The Bookmark focus on young adult library services. In addition to these thematic articles, an introduction and three reports are presented. The issue contains: (1) "In Perspective" (E. J. Josey); (2) "Young Adult Literature in the 1980's--Awesome!" (Ellin Chu); (3) "Young Adult…

  3. Lattes 'n Libraries.

    ERIC Educational Resources Information Center

    MacLeod, Leo

    1998-01-01

    Discusses providing an onsite coffee bar in a public library; includes guidelines for feasibility assessment, writing a request for proposal, and working with vendors. Weighs the advantages and disadvantages of working with big vendors and choosing a cart or a full-scale cafe. (PEN)

  4. Medicine's Library Lifeline.

    ERIC Educational Resources Information Center

    Shipman, Jean; Homan, Michael

    2003-01-01

    Discusses how librarians in the new role of "informationist" can help doctors and researches of medical information. Describes existing models of the informationist; potential benefits of working across professional boundaries outside the library; professional requirements; and unresolved issues for the new role, including potential…

  5. Library Online Systems.

    ERIC Educational Resources Information Center

    Folda, Linda; And Others

    1989-01-01

    Issues related to library online systems are discussed in six articles. Topics covered include staff education through vendor demonstrations, evaluation of online public access catalogs, the impact of integrated online systems on cataloging operations, the merits of smart and dumb barcodes, and points to consider in planning for the next online…

  6. International Library Education.

    ERIC Educational Resources Information Center

    Lowrie, Jean

    1981-01-01

    Reports the highlights of IFLA activities, including the F.I.D./I.C.A./IFLA meeting in Bellagio, Italy, June 1980, and short interest items from the Library Association (England), the Singapore Ministry of Education, and the Asian Regional Standing Committee of IFLA. (RAA)

  7. Administrative Sides of Librarying.

    ERIC Educational Resources Information Center

    Lott, Carolyn

    2003-01-01

    Discusses how the author used administrative skills learned as a school library media specialist to meet the demands of a university department chair. Topics include the influence of decisions that are made; budgeting; evaluation concerns and responsibilities; determining guidelines and goals; political concerns; and the flow of information. (LRW)

  8. Computerizing the Library.

    ERIC Educational Resources Information Center

    Chan, Jeanie; Whelan, Errol

    1988-01-01

    Discusses the development of a computerized high school library which uses CD-ROM optical storage systems. Describes hardware and software, setting up the system, preparing the online catalog, teaching information retrieval skills, and project evaluation. Notes prices of CD-ROM disks and equipment purchased. 4 references. (SV)

  9. The Special Library Budget

    ERIC Educational Resources Information Center

    Tudor, Dean

    1972-01-01

    Problems encountered by librarians in developing and living with a budget are described. PPBS (Planning-Programming-Budgeting Systems) is shown to be the most effective method of budgeting to insure acceptance and adequate funding of the library's facilities and activities. (46 references) (Author)

  10. Brain Friendly School Libraries

    ERIC Educational Resources Information Center

    Sykes, Judith Anne

    2006-01-01

    This title gives concrete practical examples of how to align school library programs and instructional practice with the six key concepts of brain-compatible learning: increasing input to the brain; increasing experiential data; multiple source feedback; reducing threat; involving students in learning decision making; and interdisciplinary unit…

  11. Modelica buildings library

    SciTech Connect

    Wetter, Michael; Zuo, Wangda; Nouidui, Thierry S.; Pang, Xiufeng

    2013-03-13

    This paper describes the Buildings library, a free open-source library that is implemented in Modelica, an equation-based object-oriented modeling language. The library supports rapid prototyping, as well as design and operation of building energy and control systems. First, we describe the scope of the library, which covers HVAC systems, multi-zone heat transfer and multi-zone airflow and contaminant transport. Next, we describe differentiability requirements and address how we implemented them. We describe the class hierarchy that allows implementing component models by extending partial implementations of base models of heat and mass exchangers, and by instantiating basic models for conservation equations and flow resistances. We also describe associated tools for pre- and post-processing, regression tests, co-simulation and real-time data exchange with building automation systems. Furthermore, the paper closes with an example of a chilled water plant, with and without water-side economizer, in which we analyzed the system-level efficiency for different control setpoints.

  12. Censorship in Public Libraries.

    ERIC Educational Resources Information Center

    Biggins, Barbara; Handsley, Elizabeth

    This paper discusses the legal obligations owed by librarians to the users of their facilities, focusing on the viewing of pornography on the Internet in the public library. The meanings commonly ascribed to the word censorship are presented. Australian federal law that governs the classification of films, videos, computer games, and publications…

  13. School Learners & Libraries.

    ERIC Educational Resources Information Center

    Karlsson, Jenni, Ed.

    This document presents papers from a conference held in November 1995 in Durban, KwaZulu-Natal, convened by the Education Policy Unit (EPU) of the University of Natal as part of research concerning the provision of library-based resources for school learners. Following an introduction are two chapters: "Identifying the Inherited Problems in…

  14. Bar Codes for Libraries.

    ERIC Educational Resources Information Center

    Rahn, Erwin

    1984-01-01

    Discusses the evolution of standards for bar codes (series of printed lines and spaces that represent numbers, symbols, and/or letters of alphabet) and describes the two types most frequently adopted by libraries--Code-A-Bar and CODE 39. Format of the codes is illustrated. Six references and definitions of terminology are appended. (EJS)

  15. Measuring Library Costs.

    ERIC Educational Resources Information Center

    Mlynarczyk, Frank, Jr.

    Based on the premise that cost measurement for a library can be performed in the same manner as for an industrial organization, this paper presents a hypothetical cost determination problem of a small company which produces bricks. A summary of the five steps taken to develop the various cost figures are: (1) Assign all cost items to the…

  16. Survivor: The Library Edition

    ERIC Educational Resources Information Center

    Curzon, Susan Carol

    2009-01-01

    Six years ago, the author shared some strategies on managing a cutback ("Budget Shortfalls," "Library Journal" 5/15/03, p. 34-35). Now, people are in an even more severe economic downturn. In this article, the author offers some additional tips on how to cope with more budget shortfalls during this recession.

  17. Revolution in the Library.

    ERIC Educational Resources Information Center

    Himmelfarb, Gertrude

    1997-01-01

    Changes in library services due to advancing information technology constitute a revolution comparable to invention of the printing press. Democratization of access to knowledge is a positive development, but it should not be confused with democratization of knowledge. This is where any system of information networking may be misleading; in…

  18. The Bionic Library.

    ERIC Educational Resources Information Center

    Billings, Harold

    1991-01-01

    Discussion of the information crisis focuses on possible new forms of library collections. Topics discussed include the rising quantity and costs of publications; improvements in access through new technologies; vendors' plans using electronic text; information flow; economics factors, including user fees; and the role of the commercial sector.…

  19. SLJ Library Computing.

    ERIC Educational Resources Information Center

    Gerhardt, Lillian N., Ed.

    1987-01-01

    Three articles include charts excerpted from "Pennsylvania Online: A Curriculum Guide for School Library Media Centers"; "Processing/Accessing Micro Software," in which Ruth Fitzgerald advocates integrating software into the card catalog; and "Microcomputer Software: A Sellers' Showcase to Physical Science Programs," in which Phyllis Levy Mandell…

  20. Libraries Are for Everyone

    ERIC Educational Resources Information Center

    Exceptional Parent, 1976

    1976-01-01

    Local libraries have resources suitable for children with disabilities which include high-interest, low-vocabulary books for children with reading problems; meeting space, speakers or materials for special interest parent groups; nonprint materials such as films and toys; and captioned motion pictures for the deaf. (SB)

  1. Light and Libraries.

    ERIC Educational Resources Information Center

    Scherer, Jeffrey

    1999-01-01

    Addresses how to integrate various types of light within the context of library design. Discusses light basics; the light spectrum; light measurement; reflectance; glare and brightness ratio; daylighting; electric lighting; and computer screens and lighting. Includes a checklist for plan review. (Author/LRW)

  2. Library Laws of Texas.

    ERIC Educational Resources Information Center

    Getz, Richard E., Comp.

    Compiled to provide a central reference point for all legislative information pertaining to libraries in the State of Texas, this publication includes all pertinent legislation as amended through the 71st Legislature, 1989, Regular Session. This update of the 1980 edition has been expanded to include statutes pertaining to the school and academic…

  3. Montessori and School Libraries

    ERIC Educational Resources Information Center

    Duffy, Michael

    2005-01-01

    This article examines the advantages of using automated media library systems and how to incorporate them in Montessori schools learning environment. Before even addressing the issue of Montessori philosophy and practice, Here, the author first address two principles: availability and accessibility. Availability is the first principle of a…

  4. Modelica buildings library

    DOE PAGES

    Wetter, Michael; Zuo, Wangda; Nouidui, Thierry S.; ...

    2013-03-13

    This paper describes the Buildings library, a free open-source library that is implemented in Modelica, an equation-based object-oriented modeling language. The library supports rapid prototyping, as well as design and operation of building energy and control systems. First, we describe the scope of the library, which covers HVAC systems, multi-zone heat transfer and multi-zone airflow and contaminant transport. Next, we describe differentiability requirements and address how we implemented them. We describe the class hierarchy that allows implementing component models by extending partial implementations of base models of heat and mass exchangers, and by instantiating basic models for conservation equations andmore » flow resistances. We also describe associated tools for pre- and post-processing, regression tests, co-simulation and real-time data exchange with building automation systems. Furthermore, the paper closes with an example of a chilled water plant, with and without water-side economizer, in which we analyzed the system-level efficiency for different control setpoints.« less

  5. Personnel Management in Libraries.

    ERIC Educational Resources Information Center

    Rubin, Richard, Ed.

    1989-01-01

    Twelve articles discuss personnel management in libraries. Topics covered include building job commitment among employers, collective bargaining, entry-level recruitment, employee turnover, performance evaluation, managing resistance to change, training problems, productivity, employee stress, compensation systems, and the Allerton Park Institute.…

  6. Middleware for Digital Libraries.

    ERIC Educational Resources Information Center

    Bacon, Jean; Hayton, Richard; Moody, Ken

    1998-01-01

    Describes a security architecture, Oasis, which runs on a middleware platform extended for asynchronous operation; shows how the interoperation of independently developed services may be supported under the Oasis architecture. Uses the provision of digital academic library services as an example. (Author/AEF)

  7. Women, Power, and Libraries.

    ERIC Educational Resources Information Center

    Schuman, Patricia Glass

    1984-01-01

    Discusses the concept of power in the context of women and the library profession, citing views of power by Max Weber, John Kenneth Galbraith, Letty Cottin Pogrebin, and Rosabeth Moss Kantor. Male power and female submission, defining power, organizing for power, and sharing power are highlighted. A 12-item bibliography is included. (EJS)

  8. The Virtual Library

    ERIC Educational Resources Information Center

    Valenza, Joyce Kasman

    2006-01-01

    Today's school libraries must meet student needs as both a physical and virtual space. Existing both offline and online, they must offer around-the-clock access as well as instruction and guidance that support the face-to-face interactions of students with librarians and classroom teachers. Although students are often technologically proficient,…

  9. Fire Protection for Libraries.

    ERIC Educational Resources Information Center

    Fortson-James, Judith

    1981-01-01

    This overview of preventive measures that can be taken to help minimize damage to library materials from fire discusses the advantages, disadvantages, dangers, and comparative costs of several types of sprinkler systems, including high-expansion foam, total-flooding, dry- and wet-pipe systems, and on-off sprinkler heads. Five references are…

  10. Facility Focus: Libraries.

    ERIC Educational Resources Information Center

    College Planning & Management, 2000

    2000-01-01

    Describes school library designs at four universities where each addresses different types of modernization needs. Described are designs that provide modern learning environments; knit the campus together without destroying architectural heritage of the school; compliments a 50's design while maximizing comfort, privacy, and group interaction; and…

  11. Fundamentals of Library Instruction

    ERIC Educational Resources Information Center

    McAdoo, Monty L.

    2012-01-01

    Being a great teacher is part and parcel of being a great librarian. In this book, veteran instruction services librarian McAdoo lays out the fundamentals of the discipline in easily accessible language. Succinctly covering the topic from top to bottom, he: (1) Offers an overview of the historical context of library instruction, drawing on recent…

  12. Haselwood Library, Olympic College.

    ERIC Educational Resources Information Center

    Design Cost Data, 2001

    2001-01-01

    Showcases the open-book design of a 36,000-square-foot library and media center for Olympic College in Bremerton, Washington. Discusses the architectural design requirments and need to phase construction, as well as costs and project history. Includes floor plan, general description, photos, and a list of manufacturers and suppliers used for the…

  13. Taking Library Leadership Personally

    ERIC Educational Resources Information Center

    Davis, Heather; Macauley, Peter

    2011-01-01

    This paper outlines the emerging trends for leadership in the knowledge era. It discusses these within the context of leading, creating and sustaining the performance development cultures that libraries require. The first step is to recognise that we all need to take leadership personally no matter whether we see ourselves as leaders or followers.…

  14. Excellence in Library Management.

    ERIC Educational Resources Information Center

    Naulty, Deborah

    By emulating traits of high-performing corporations such as those described in the book "In Search of Excellence," the library/information profession can also reach the goal of excellence. Attributes characterizing excellent companies include exhibiting a bias for action; maintaining quality service through closeness to the customer;…

  15. The Hungarian Library Law.

    ERIC Educational Resources Information Center

    1976

    This booklet includes the Law-Decree No. 15 on Libraries issued by the Presidium of the Hungarian People's Republic in 1976 and the decree of the Council of Ministers on its implementation. The purpose of the decree is to further the fulfilment of citizens' cultural demands, and meet the needs for special literature of both citizens and corporate…

  16. People Need Libraries.

    ERIC Educational Resources Information Center

    Queens Borough Public Library, Jamaica, NY.

    This annual report of the Queens Borough Public Library for 1976-77 focuses on the cooperative efforts it employed to maximize its services in the face of New York City's fiscal crisis. Though the staff was reduced by nearly 28 percent and hours were decreased by nearly 44 percent, circulation and reference statistics show only a 7 percent…

  17. School Library Nostalgias

    ERIC Educational Resources Information Center

    Hochman, Jessica

    2016-01-01

    This paper explores nostalgia as both a limiting cultural force in the lives of school librarians and a practice that can be used to more accurately portray library work. The stereotype of the shushing, lone school librarian, based on restorative nostalgia, is related to a nostalgic oversimplification of the school librarian's historical role.…

  18. Wayfinding in Libraries.

    ERIC Educational Resources Information Center

    Beck, Susan Gilbert

    1996-01-01

    Discusses recommendations for designing or redesigning library buildings for easy navigability. Signage, maps, collection arrangements, and placement of emergency exits must take into account observed traffic patterns, spatial or objective orientations of individual patrons, and patrons with disabilities. Contains 63 references. (BEW)

  19. Robot Vision Library

    NASA Technical Reports Server (NTRS)

    Howard, Andrew B.; Ansar, Adnan I.; Litwin, Todd E.; Goldberg, Steven B.

    2009-01-01

    The JPL Robot Vision Library (JPLV) provides real-time robot vision algorithms for developers who are not vision specialists. The package includes algorithms for stereo ranging, visual odometry and unsurveyed camera calibration, and has unique support for very wideangle lenses

  20. Academic Library Reference Services.

    ERIC Educational Resources Information Center

    Batt, Fred

    This examination of the philosophy and objectives of academic library reference services provides an overview of the major reference approaches to fulfilling the following primary objectives of reference services: (1) providing accurate answers to patrons' questions and/or helping patrons find sources to pursue their research needs; (2) building…

  1. Designing Secure Library Networks.

    ERIC Educational Resources Information Center

    Breeding, Michael

    1997-01-01

    Focuses on designing a library network to maximize security. Discusses UNIX and file servers; connectivity to campus, corporate networks and the Internet; separation of staff from public servers; controlling traffic; the threat of network sniffers; hubs that eliminate eavesdropping; dividing the network into subnets; Switched Ethernet;…

  2. Planetary Image Geometry Library

    NASA Technical Reports Server (NTRS)

    Deen, Robert C.; Pariser, Oleg

    2010-01-01

    The Planetary Image Geometry (PIG) library is a multi-mission library used for projecting images (EDRs, or Experiment Data Records) and managing their geometry for in-situ missions. A collection of models describes cameras and their articulation, allowing application programs such as mosaickers, terrain generators, and pointing correction tools to be written in a multi-mission manner, without any knowledge of parameters specific to the supported missions. Camera model objects allow transformation of image coordinates to and from view vectors in XYZ space. Pointing models, specific to each mission, describe how to orient the camera models based on telemetry or other information. Surface models describe the surface in general terms. Coordinate system objects manage the various coordinate systems involved in most missions. File objects manage access to metadata (labels, including telemetry information) in the input EDRs and RDRs (Reduced Data Records). Label models manage metadata information in output files. Site objects keep track of different locations where the spacecraft might be at a given time. Radiometry models allow correction of radiometry for an image. Mission objects contain basic mission parameters. Pointing adjustment ("nav") files allow pointing to be corrected. The object-oriented structure (C++) makes it easy to subclass just the pieces of the library that are truly mission-specific. Typically, this involves just the pointing model and coordinate systems, and parts of the file model. Once the library was developed (initially for Mars Polar Lander, MPL), adding new missions ranged from two days to a few months, resulting in significant cost savings as compared to rewriting all the application programs for each mission. Currently supported missions include Mars Pathfinder (MPF), MPL, Mars Exploration Rover (MER), Phoenix, and Mars Science Lab (MSL). Applications based on this library create the majority of operational image RDRs for those missions. A

  3. Libraries in California: MedlinePlus

    MedlinePlus

    ... 626-2778 http://www.marshallmedical.org/library Davis University of California at Davis Carlson Health Sciences Library ... ucsf.edu/library-services/ Fullerton Marshall B. Ketchum University MB Ketchum Memorial Library ILL 2575 Yorba Linda ...

  4. Directory of Library and Related Organizations.

    ERIC Educational Resources Information Center

    Bowker Annual Library and Book Trade Almanac, 1999

    1999-01-01

    Provides a directory of the following types of library and related organizations in the United States and Canada: "Networks, Consortia and Other Cooperative Library Organizations"; "National Library and Information-Industry Associations"; "State, Provincial, and Regional Library Associations"; "State and…

  5. Library Orientation and Instruction for Medical Students.

    ERIC Educational Resources Information Center

    Iroka, Luke A.

    1989-01-01

    Briefly describes the methods used to provide library orientation (an introduction to the physical plant, policies, procedures and resources of the library) and library instruction (bibliographic and research skills) in Nigerian medical libraries. (five references) (CLB)

  6. Libraries in Kentucky: MedlinePlus

    MedlinePlus

    ... this page: https://medlineplus.gov/libraries/kentucky.html Libraries in Kentucky To use the sharing features on ... JavaScript. Bowling Green WESTERN KENTUCKY UNIVERSITY Dept. of Library Public Services/WKU Libraries 1906 College Heights Blvd # ...

  7. Libraries in Saskatchewan: MedlinePlus

    MedlinePlus

    ... this page: https://medlineplus.gov/libraries/saskatchewan.html Libraries in Saskatchewan To use the sharing features on this page, please enable JavaScript. Prince Albert PAPHR Library Library, Victoria Hospital 1200 - 24th Street West Prince ...

  8. Statistical evaluation of SAGE libraries: consequences for experimental design.

    PubMed

    Ruijter, Jan M; Van Kampen, Antoine H C; Baas, Frank

    2002-10-29

    Since the introduction of serial analysis of gene expression (SAGE) as a method to quantitatively analyze the differential expression of genes, several statistical tests have been published for the pairwise comparison of SAGE libraries. Testing the difference between the number of specific tags found in two SAGE libraries is hampered by the fact that each SAGE library is only one measurement: the necessary information on biological variation or experimental precision is not available. In the currently available tests, a measure of this variance is obtained from simulation or based on the properties of the tag distribution. To help the user of SAGE to decide between these tests, five different pairwise tests have been compared by determining the critical values, that is, the lowest number of tags that, given an observed number of tags in one library, needs to be found in the other library to result in a significant P value. The five tests included in this comparison are SAGE300, the tests described by Madden et al. (Oncogene 15: 1079-1085, 1997) and by Audic and Claverie (Genome Res 7: 986-995, 1997), Fisher's Exact test, and the Z test, which is equivalent to the chi-squared test. The comparison showed that, for SAGE libraries of equal as well as different size, SAGE300, Fisher's Exact test, Z test, and the Audic and Claverie test have critical values within 1.5% of each other. This indicates that these four tests will give essentially the same results when applied to SAGE libraries. The Madden test, which can only be used for libraries of similar size, is, with 25% higher critical values, more conservative, probably because the variance measure in its test statistic is not appropriate for hypothesis testing. The consequences for the choice of SAGE library sizes are discussed.

  9. Library Hospitality: Some Preliminary Considerations

    ERIC Educational Resources Information Center

    Johnson, Eric D. M.; Kazmer, Michelle M.

    2011-01-01

    Library scholars and practitioners have frequently reflected on the various factors that in combination make up a hospitable library, but there has been little theoretical synthesis of the notion of the library as a place of hospitality. The hospitality industry provides a rich vein of theoretical material from which to draw definitions of…

  10. Maine School Library Facilities Handbook.

    ERIC Educational Resources Information Center

    Maine Association of School Libraries.

    This handbook provides guidance to school library specialists and architects for planning new or renovated library facilities that will meet the changing resource and technology needs of students and the community. An overview is provided of the essential library areas, including layout, structural, and climate control needs; the internal…

  11. Professional Specialists in Academic Libraries.

    ERIC Educational Resources Information Center

    Cottam, Keith M.

    As research libraries have grown, a trend has developed to recruit specialists to support the administrative and technical functions of the library. Business, planning, automation, personnel, and facilities specialists are among those currently employed. Libraries which utilize such specialists experience significant gains in flexibility to…

  12. Depository Libraries and Public Services.

    ERIC Educational Resources Information Center

    Kessler, Ridley

    1998-01-01

    Discusses the Wright State University (Ohio) Library policy directive on customer service, and suggests this document as a model to follow in setting up service standards or guidelines for depository-library services. Draft-depository library public-service guidelines for government information in electronic format are appended. (JAK)

  13. Library Buildings 1967-1968.

    ERIC Educational Resources Information Center

    Berriman, S. G., Ed.

    This booklet describes 21 libraries completed in England during 1967-68. Photographs and floor plans illustrate structural details, and a descriptive section presents the history of each library and comments on those design features considered both functional and attractive. A table summarizes relevant data on each library. (MLF)

  14. Dynamic Digital Libraries for Children.

    ERIC Educational Resources Information Center

    Theng, Yin Leng; Mohd-Nasir, Norliza; Buchanan, George; Fields, Bob; Thimbleby, Harold; Cassidy, Noel

    The design of systems, including digital libraries, is often inspired by what technology makes possible. In user-centered design, design emphasizes users, their tasks and needs. The majority of current digital libraries are not designed for children. For digital libraries to be popular with children, they need to be fun and easy-to-use. This paper…

  15. Library Fundraising: Models for Success.

    ERIC Educational Resources Information Center

    Burlingame, Dwight F., Ed.

    This book is a compilation of advice on library fundraising through the presentation of real-life case studies. Contributors offer both recommendations and caveats based on their firsthand fundraising experiences in public and college libraries. Libraries of varying size and financial scale are represented in discussions of pursuing grants,…

  16. Education Libraries: An International Perspective.

    ERIC Educational Resources Information Center

    Galler, Anne M.

    1997-01-01

    Explains what an education library is and describes methods used in seeking out such libraries on an international basis. Libraries in Sweden, Finland, Australia, Hong Kong, Singapore, and Canada are described, including address, World Wide Web page, mission, history, clientele, type of collection, services, publications, and databases. (LRW)

  17. Position Analysis of Library Assistants.

    ERIC Educational Resources Information Center

    Defa, Dennis R.

    1995-01-01

    Issues of maintaining equity of classification and salary for library assistants across a university library system and in relation to other university departments are addressed. A 1989 job analysis of library assistant positions at the University of Utah resulted in the reclassification of positions and an increase in salary implemented over two…

  18. Beyond Decoding: Literacy and Libraries.

    ERIC Educational Resources Information Center

    Bookmark, 1992

    1992-01-01

    This issue contains 21 articles discussing library-sponsored literacy programs, tutoring and programming techniques, and state and national efforts. The articles include: (1) "Beyond Decoding: Literacy and Libraries--Introduction" (Amy Spaulding); (2) "Libraries: Natural Centers for Literacy" (Jacqueline Cook); (3) "Kids…

  19. Library Management Tips that Work

    ERIC Educational Resources Information Center

    Smallwood, Carol, Ed.

    2011-01-01

    There's no shortage of library management books out there--but how many of them actually tackle the little details of day-to-day management, the hard-to-categorize things that slip through the cracks of a larger handbook? "Library Management Tips that Work" does exactly that, addressing dozens of such issues facing library managers, including: (1)…

  20. Digital Libraries on the Internet.

    ERIC Educational Resources Information Center

    Sharon, Taly; Frank, Ariel J.

    This paper discusses digital libraries on the Internet. The resource repository hierarchy, consisting of two major paradigms, search engines (SEs) and digital libraries, is presented. SEs are classified into three categories: basic-SE, directory, and meta-SE. The following six major characteristics of a library are summarized: collection of data…

  1. Managing Quality: TQM in Libraries.

    ERIC Educational Resources Information Center

    Riggs, Donald E.

    1993-01-01

    Discusses the use of total quality management (TQM) principles in libraries. Topics addressed include commitment from the library director; strategic planning; training needs for library staff; the identification and selection of targeted areas that would benefit from TQM; quality improvement teams; analysis; proposed solutions; and evaluation…

  2. Chat Widgets for Science Libraries

    ERIC Educational Resources Information Center

    Meier, John J.

    2008-01-01

    This paper describes chat widgets, chunks of code that can be embedded on a web site to appear as an instant messaging system, and how they can be used on a science library web site to better serve library users. Interviews were conducted concerning experiences at science and humanities libraries and more similarities than differences were…

  3. The Marine Corps University Library.

    ERIC Educational Resources Information Center

    Ramkey, Carol E.

    2001-01-01

    Describes the Marine Corps University (Virginia) Library's collections and reserves. States that the library's resources focus on military doctrine, history, arts, and sciences, and that they include Web- and CD-ROM-based specialized military databases. Describes the library's mission to serve the university community and Marine Corps patrons…

  4. Extended Library Hours. SPEC Kit.

    ERIC Educational Resources Information Center

    Steele, Patricia Ann, Comp.; Walters, Carolyn, Comp.

    2001-01-01

    This SPEC (Systems and Procedures Exchange Center) Kit presents the results of a survey of Association of Research Libraries (ARL) member libraries designed to provide a description of how they are responding to demands for greater hours of access and service. Survey responses indicate what hours of access and service libraries are providing and…

  5. The Florida Library History Project.

    ERIC Educational Resources Information Center

    Jasper, Catherine; McCook, Kathleen de la Pena

    The Florida Library History Project (FLHP) began in January 1998. Letters requesting histories were sent to all public libraries in Florida with follow-up letters sent after an initial response was received from the libraries. E-mail messages were sent out to FL-LIB listservs encouraging participation in the project. A poster session was presented…

  6. IEEE Conference Publications in Libraries.

    ERIC Educational Resources Information Center

    Johnson, Karl E.

    1984-01-01

    Conclusions of surveys (63 libraries, OCLC database, University of Rhode Island users) assessing handling of Institute of Electrical and Electronics Engineers (IEEE) conference publications indicate that most libraries fully catalog these publications using LC cataloging, and library patrons frequently require series access to publications. Eight…

  7. A City of Libraries: Paris.

    ERIC Educational Resources Information Center

    Whitten, Benjamin

    1983-01-01

    This overview of Parisian libraries includes descriptions of the Bibliotheque National, Bibliotheque Mazarine, Library of the Sorbonne, Bibliotheque Sainte Genevieve, Bibliotheque de l'Arsenal, Bibliotheque Historique de la Ville de Paris, Bibliotheque Forney, Library of the Opera, Bibliotheque Publique d'Information, and the forthcoming…

  8. An Anthropologist in the Library

    ERIC Educational Resources Information Center

    Carlson, Scott

    2007-01-01

    Nancy Fried Foster was an anthropologist hired by University of Rochester's library to study its undergraduates, to help shed light on how they do their research and write papers, and how they spend their days. The results of the study helped guide a library renovation, influenced a Web-site redesign, led to changes in the way the library markets…

  9. Five Libraries Capture Architectural Awards.

    ERIC Educational Resources Information Center

    American Libraries, 1985

    1985-01-01

    Presents detailed look at University of Michigan Law, Folger Shakespeare, Vail Public, San Francisco University High School, and New York University Graduate School of Business Libraries, winners of 11th Library Buildings Award Program which included two renovations, two additions, and one new facility. Other notable library design projects are…

  10. Rural Libraries, Volume XIV, 1994.

    ERIC Educational Resources Information Center

    Pratt, Mary Lou, Ed.

    1994-01-01

    The 2 issues in this volume contain 10 articles on rural libraries and information access in rural America. Topics include telecommunications and distance education in Nebraska, the future of small rural public libraries, federal programs to improve rural access to information, outreach issues for public libraries, and the role of information in…

  11. ARL Profiles: Research Libraries 2010

    ERIC Educational Resources Information Center

    Potter, William Gray; Cook, Colleen; Kyrillidou, Martha

    2011-01-01

    The current ARL report summarizes a multi-year effort that captures evidence in the form of narrative profiles as it delivers the message of the value and contributions of research libraries during transformative times. When ARL library directors were interviewed in 2005 and asked to describe a research library in the 21st century, there was…

  12. Library Technicians in the USA.

    ERIC Educational Resources Information Center

    Johnson, Ian M.

    Based on discussions with librarians, library personnel managers, and instructors involved in junior college library technician programs in eight cities, this report of a September 1980 study tour describes the training of library technicians in the United States. Sections cover aims of the study tour; planning the tour; the organization of…

  13. How to Survive Library Renovation.

    ERIC Educational Resources Information Center

    Lambert, Linda Stern

    1992-01-01

    Describes the renovation of the library at Walnut Hill School for the Arts (Natick, Massachusetts). Topics discussed include initial planning; packing up the collection for storage; dealing with construction delays while maintaining some library service; moving into the new space; student and teacher reactions; and the effects on library use. (LRW)

  14. Crerar/Chicago Library Merger.

    ERIC Educational Resources Information Center

    Cairns, Paul M.

    1986-01-01

    Describes steps in survey project that supplied information for contemplated merger of two libraries by estimating number of volumes and titles and duplication between John Crerar Library collections and University of Chicago Library science collections. Survey's findings for volume duplication are analyzed by subject groupings and by books and…

  15. Microcomputers in the Anesthesia Library.

    ERIC Educational Resources Information Center

    Wright, A. J.

    The combination of computer technology and library operation is helping to alleviate such library problems as escalating costs, increasing collection size, deteriorating materials, unwieldy arrangement schemes, poor subject control, and the acquisition and processing of large numbers of rarely used documents. Small special libraries such as…

  16. Standards for vision science libraries

    PubMed Central

    2000-01-01

    The minimum levels of staffing, services, budget, and technology that should be provided by a library specializing in vision science are presented. The scope and coverage of the collection is described as well. These standards may be used by institutions establishing libraries or by accrediting bodies reviewing existing libraries. PMID:10928708

  17. The ACL Message Passing Library

    SciTech Connect

    Painter, J.; McCormick, P.; Krogh, M.; Hansen, C.; Colin de Verdiere, G.

    1995-09-01

    This paper presents the ACL (Advanced Computing Lab) Message Passing Library. It is a high throughput, low latency communications library, based on Thinking Machines Corp.`s CMMD, upon which message passing applications can be built. The library has been implemented on the Cray T3D, Thinking Machines CM-5, SGI workstations, and on top of PVM.

  18. Celebrate International School Library Day

    ERIC Educational Resources Information Center

    Braxton, Barbara

    2004-01-01

    The Fourth Monday in October is International School Library Day (ISLD)--an opportunity for school libraries around the world to celebrate the contribution they make to the education of the children in their care. International School Library Day was proclaimed in 1999 by Dr Blanche Woolls, president of the International Association of School…

  19. Library Automation: Guidelines to Costing.

    ERIC Educational Resources Information Center

    Ford, Geoffrey

    As with all new programs, the costs associated with library automation must be carefully considered before implementation. This document suggests guidelines to be followed and areas to be considered in the costing of library procedures. An existing system model has been suggested as a standard (Appendix A) and a classification of library tasks…

  20. Technology's Impact on Library Operations.

    ERIC Educational Resources Information Center

    Jui, Doris

    For the last 58 years, automation has helped to enhance the library system; library operations such as circulation, cataloging, acquisitions, and serials have changed significantly due to technology. Circulation control is often the first activity a library considers automating. In addition to loan transactions, an automated circulation system can…

  1. Library Science Instruction: A Credo.

    ERIC Educational Resources Information Center

    Sable, Martin H.

    1988-01-01

    Discusses the need to treat library science teaching as a whole, rather than focusing on methodology alone, and addresses five areas that constitute library education: physical requirements, the psycho-social environment, teacher qualifications and duties, teachers' professional attitudes, and suggestions for improving the library science…

  2. The Pulse of Library Education.

    ERIC Educational Resources Information Center

    Gaughan, Tom

    1992-01-01

    This second discussion of a survey of library schools and library education examines a variety of topics, including student applications and enrollment; student placement and student satisfaction; budgets; external funding; economic problems; faculty research productivity; faculty retirements; position of the library school within the university;…

  3. Customer Satisfaction with Public Libraries.

    ERIC Educational Resources Information Center

    D'Elia, George; Rodger, Eleanor Jo

    1996-01-01

    Surveys conducted in 142 urban public libraries examined customer satisfaction, comparisons with other libraries, and factors affecting satisfaction. Overall, customers were satisfied with their libraries but experienced different levels of satisfaction based on convenience, availability of materials and information, and services facilitating…

  4. Information Activities in Medical Library : Tokyo Women's Medical College Library

    NASA Astrophysics Data System (ADS)

    Nishioka, Masayuki

    The library facilities, resource materials, training of librarians and so on are described at first. The library collection is that of middle sized medical library. However, since the facilities are not enough to handle it, it is necessary for the library to be supplemented by information services. Then primary information services such as reading of materials, interlibrary loan and journal acquisition system of the recent issues for each laboratory is outlined. Secondary information services centered around on-line information retrieval service, contents sheet service and preparation of index cards are also described. What a medical library should be is considered in terms of its relation to information services.

  5. Welcome to the National Wetlands Research Center Library: Not Just Another Library-A Special Library

    USGS Publications Warehouse

    Broussard, Linda

    2007-01-01

    Libraries are grouped into four major types: public, school, academic, and special. The U.S. Geological Survey's (USGS) National Wetlands Research Center (NWRC) library is classified as a special library because it is sponsored by the Federal government, and the collections focus on a specific subject. The NWRC library is the only USGS library dedicated to wetland science. Library personnel offer expert research services to meet the informational needs of NWRC scientists, managers, and support personnel. The NWRC library participates in international cataloging and resource sharing, which allows libraries from throughout the world to borrow from its collections. This sharing facilitates the research of other governmental agencies, universities, and those interested in the study of wetlands.

  6. Public Library Automation Report: Circulation [and] Appendix.

    ERIC Educational Resources Information Center

    Gotanda, Masae; And Others

    An online circulation system--ULISYS (the Universal Library System Ltd.) manufactured by Digital Equipment Corporation (DEC)--is being installed in the Hawaii State Library, Kaneohe Regional Library, Kailua Community Library and Waimanalo Community/School Library. These libraries are the first users of a statewide online circulation system…

  7. Florida Library Directory with Statistics, 1996.

    ERIC Educational Resources Information Center

    Florida Dept. of State, Tallahassee. Div. of Library and Information Services.

    This publication is a directory of Florida libraries and related organizations, and contains statistical data for Florida public libraries for fiscal year 1994-95. The report lists members of the State Library Council, Florida State Advisory Council on Libraries, Florida Library Network Council, Staff Directory, State Library of Florida…

  8. Academic and Public Library Buildings, 1986.

    ERIC Educational Resources Information Center

    Fox, Bette-Lee; And Others

    1986-01-01

    Three articles on library buildings present Library Journal's annual architectural survey of completed public and academic library buildings and library projects in progress; guidelines for leasing a shared library facility, and a description of a successful public library building project in Michigan are also discussed. (EM)

  9. Florida Library Directory with Statistics, 1999.

    ERIC Educational Resources Information Center

    Taylor-Furbee, Sondra, Comp.; Kellenberger, Betsy, Comp.

    The first section of this directory of Florida libraries with statistics provides information on Florida Division of Library and Information Services library organizations, councils, and associations, including: directories of State Library Council, Library Services and Technology Act Advisory Council, Florida Library Network Council, and Division…

  10. Directory of Library and Related Organizations.

    ERIC Educational Resources Information Center

    Bowker Annual Library and Book Trade Almanac, 1998

    1998-01-01

    Lists networks, consortia, and other cooperative library organizations; national library and information-industry associations--United States and Canada; state, provincial, and regional associations; state and provincial library agencies; state school library media associations; international library associations; and foreign library associations.…

  11. Directory of Library and Related Organizations.

    ERIC Educational Resources Information Center

    Bowker Annual Library and Book Trade Almanac, 2001

    2001-01-01

    Lists networks, consortia, and other cooperative library organizations; national library and information-industry associations in the U.S. and Canada; state, provincial, and regional library associations and agencies; state school library media associations; international library associations; and foreign library associations. (LRW)

  12. Art Libraries: Creating Access to Unique Collections

    ERIC Educational Resources Information Center

    Falls, Sarah E.

    2009-01-01

    Art libraries face similar issues to other types of libraries during the digital transition but have unique twists driven by the needs of their collections. Art library information seekers may possess a sense of what an art library is: a library, set apart, to support the study of art and art history. For art libraries, it is the collection,…

  13. Library of the Year 2008: Laramie County Library System, Wyoming--The Impact Library

    ERIC Educational Resources Information Center

    Berry, John N., III

    2008-01-01

    This article features Laramie County Library System (LCLS) of Cheyenne, Wyoming, which is named as Gale/"Library Journal" 2008 Library of the Year. It is not just strong, effective publicity or the fine new building or even a staff built around its ability to connect with the people, although all of those things add to the impact of…

  14. University Libraries and Other General Research Libraries Section. General Research Libraries Division. Papers.

    ERIC Educational Resources Information Center

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

    Papers on university and other research libraries, presented at the 1983 International Federation of Library Associations (IFLA) conference, include: (1) "The Impact of Technology on Users of Academic and Research Libraries," in which C. Lee Jones (United States) focuses on the impact of technical advances in computing and…

  15. Evaluated teletherapy source library

    DOEpatents

    Cox, Lawrence J.; Schach Von Wittenau, Alexis E.

    2000-01-01

    The Evaluated Teletherapy Source Library (ETSL) is a system of hardware and software that provides for maintenance of a library of useful phase space descriptions (PSDs) of teletherapy sources used in radiation therapy for cancer treatment. The PSDs are designed to be used by PEREGRINE, the all-particle Monte Carlo dose calculation system. ETSL also stores other relevant information such as monitor unit factors (MUFs) for use with the PSDs, results of PEREGRINE calculations using the PSDs, clinical calibration measurements, and geometry descriptions sufficient for calculational purposes. Not all of this information is directly needed by PEREGRINE. It also is capable of acting as a repository for the Monte Carlo simulation history files from which the generic PSDs are derived.

  16. Geodesic IO Library

    SciTech Connect

    2011-03-15

    GIO is an application programmer interface (API) or library for high performance IO that is designed for climate models that operate on a geodesic grid. GIO uses a combination of configuration files and API calls to define the mapping of internal model data to output variables in standard climate data formats. The mapping from model data to model output includes method of data slicing, aggregation, and linearization using a morton ordering approach. The data is then persisted through a standard interface that can be implemented using several different high level parallel libraries. Both Parallel NetCDF and NetCDF4 interfaces are provided. GIO is designed to run on supercomputing systems or multi-processor clusters with parallel file systems.

  17. Persistent heap Management library

    SciTech Connect

    2012-01-17

    PERM is a C library for persistent heap management and is intended for use with a dynamic-memory allocator (e.g. malloc, free). The PERM memory allocator replaces the standard C dynamic memory allocation functions with compatible versions that provide persistent memory to application programs. Memory allocated with the PERM allocatory will persist between program invocations after a call to a checkpoint function. This function essentially saves the state of the heap and registered global variables to a file which may reside in flash memory or other node local storage. A few other functions are also provided by the library to manage checkpoint files. Global variables in an application can be marked persistent and be included in a checkpoint by using a compiler attribute defined as PERM. The PERM checkpoint methof is not dependent on the programming model ans works with distributed memory or shared memory programs.

  18. CleanEST: a database of cleansed EST libraries.

    PubMed

    Lee, Byungwook; Shin, Gwangsik

    2009-01-01

    The EST division of GenBank, dbEST, is widely used in many applications such as gene discovery and verification of exon-intron structure. However, the use of EST sequences in the dbEST libraries is often hampered by inconsistent terminology used to describe the library sources and by the presence of contaminated sequences. Here, we describe CleanEST, a novel database server that classified dbEST libraries and removes contaminants. We classified all dbEST libraries according to species and sequencing center. In addition, we further classified human EST libraries by anatomical and pathological systems according to eVOC ontologies. For each dbEST library, we provide two different cleansed sequences: 'pre-cleansed' and 'user-cleansed'. To generate pre-cleansed sequences, we cleansed sequences in dbEST by alignment of EST sequences against well-known contamination sources: UniVec, Escherichia coli, mitochondria and chloroplast (for plant). To provide user-cleansed sequences, we built an automatic user-cleansing pipeline, in which sequences of a user-selected library are cleansed on-the-fly according to user-selected options. The server is available at http://cleanest.kobic.re.kr/ and the database is updated monthly.

  19. Feature Characterization Library

    SciTech Connect

    Doyle, Wendy; Gentile, Ann; McCoy, Renata

    2006-08-03

    FCLib is a data analysis toolkit constructed to meet the needs of data discovery in large-scale, spatio-temporal data such as finite element simulation data. FCLib is a C library toolkit of building blocks that can be assembled into complex analyses. Important features of FCLib include the following: (1) Support of feature-based analysis, (2) minimization of low-oevel processing, (3) ease of use, and (4) applicable to the wide variety of science domains.

  20. Land Treatment Digital Library

    USGS Publications Warehouse

    Pilliod, David S.

    2009-01-01

    Across the country, public land managers make hundreds of decisions each year that influence landscapes and ecosystems within the lands they manage. Many of these decisions involve vegetation manipulations known as land treatments. Land treatments include activities such as removal or alteration of plant biomass, seeding burned areas, and herbicide applications. Data on these land treatments are usually stored at local offices, and gathering information across large spatial areas can be difficult. There is a need to centralize and store treatment data for Federal agencies involved in land treatments because these data are useful to land managers for policy and management and to scientists for developing sampling designs and studies. The Land Treatment Digital Library (LTDL) was created by the U.S. Geological Survey (USGS) to catalog information about land treatments on Federal lands in the western United States for all interested parties. The flexible framework of the library allows for the storage of a wide variety of data in different formats. The LTDL currently stores previously established land treatments or what often are called legacy data. The project was developed and has been refined based on feedback from partner agencies and stakeholders, with opportunity for the library holdings to expand as new information becomes available. The library contains data in text, tabular, spatial, and image formats. Specific examples include project plans and implementation reports, monitoring data, spatial data files from geographic information systems, digitized paper maps, and digital images of land treatments. The data are entered by USGS employees and are accessible through a searchable web site. The LTDL can be used to respond to information requests, conduct analyses and other forms of information syntheses, produce maps, and generate reports for DOI managers and scientists and other authorized users.