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PubMed1986

Fast Inter Library Loans and Statistics, enhanced version 2.0.

F.I.L.L.S. is a library-specific software package developed by librarians for library staff with little or no computer experience. MacNeal Hospital's Health Science Resource Center designed F.I.L.L.S. to allow libraries to save 60 percent of the time devoted to the interlibrary loan function while improving service to users. As a management tool, F.I.L.L.S. creates a dozen (12) preprogrammed reports that provide invaluable information such as Number of Requests for Periodicals, including copyright information; which libraries are borrowed from frequently; and which libraries provide the fastest or slowest service in filling loan requests. The article describes F.I.L.L.S., its capabilities and its limitations in greater detail.

Computers↗

PubMed2001

Redefining reference in an academic health sciences library: planning for change.

Deciding that changes in the pattern of questions at the reference desk required focused consideration, the reference librarians at the Health Sciences Library of the University at Buffalo held a planning retreat. Technology-induced changes in the information-seeking behavior and reference needs of the library's clientele caused a reassessment of how these needs could best be met and what is the best use of librarians' time. The librarians considered current trends in reference in other academic libraries, the specific needs of the clientele of the Health Sciences Library, and the strengths and expertise of the library staff. The results of this structured discussion produced ideas for redefining reference to provide customized services for the clients and environment.

Academic Medical Centers↗

PubMed2005

Relationship marketing in a hospital library.

This article explores relationship marketing as adopted by staff of the Forbes Medical Library at The Children's Hospital in Denver. It provides a broad overview of relationship marketing along with its applications in libraries, and a description of how the library staff has used specific relationships with different hospital groups to enhance library service. The examples illustrate the importance of persistence, patience, and flexibility when consciously developing relationships between a library and individuals or groups.

Colorado↗

PubMed2026

A trainable language model with potential to modulate translation rates in non-model organisms by generating upstream untranslated region sequence libraries.

Tuning protein expression in non-model organisms is often constrained by the lack of validated genetic parts and predictive design tools. Translational tuning through the modulation of upstream untranslated regions (5'-UTRs) offers a potentially organism-agnostic route, but existing methods typically rely on mechanistic assumptions, prior knowledge that may not be available in non-model contexts, or the screening of sequence libraries. Here, we present a simple generative approach for creating synthetic 5'-UTR libraries based solely on the genomic sequence statistics of any desired organism. The method uses a sliding-window n-gram language model applied to native 5'-UTR sequences to produce novel sequences that preserve organism-specific base distributions and motifs without hard-coding specific motifs or mechanistic rules into inflexible statistical templates. We have applied this approach to the model bacterium Escherichia coli and the non-model probiotic Limosilactobacillus reuteri. Libraries of approximately 1,000 sequences were generated for each organism, from which about 100 unique sequences were experimentally tested for translation of a fluorescent reporter protein. In both organisms, the synthetic libraries yielded a broad range of translation levels from this relatively small number of tested variants. Sequences derived from an organism's own genomic statistics provided a more uniformly distributed range of translation rates in that organism than sequences derived from the other species. Correlations of individual sequence performance across the two species were weak, and thermodynamic predictions of ribosome binding strength showed very little predictive power, especially in the non-model L. reuteri. The results demonstrate that simple statistical language model approaches applied to genomic data can generate functional translational regulatory sequence libraries without detailed mechanistic knowledge or explicit reference to consensus motifs. The approach requires minimal computational resources, avoids reproducing native sequences, and can be readily applied to any organism with a sequenced genome. This strategy may lower technical barriers to expression tuning in non-model organisms.

5' Untranslated Regions↗

PubMed2006

Gene expression from random libraries of yeast promoters.

Genomewide techniques to assay gene expression and transcription factor binding are in widespread use, but are far from providing predictive rules for the function of regulatory DNA. To investigate more intensively the grammar rules for active regulatory sequence, we made libraries from random ligations of a very restricted set of sequences. Working with the yeast Saccharomyces cerevisiae, we developed a novel screen based on the sensitivity of ascospores lacking dityrosine to treatment with lytic enzymes. We tested two separate libraries built by random ligation of a single type of activator site either for a well-characterized sporulation factor, Ndt80, or for a new sporulation-specific regulatory site that we identified and several neutral spacer elements. This selective system achieved up to 1:10(4) enrichment of the artificial sequences that were active during sporulation, allowing a high-throughput analysis of large libraries of synthetic promoters. This is not practical with methods involving direct screening for expression, such as those based on fluorescent reporters. There were very few false positives, since active promoters always passed the screen when retested. The survival rate of our libraries containing roughly equal numbers of spacers and activators was a few percent that of libraries made from activators alone. The sequences of approximately 100 examples of active and inactive promoters could not be distinguished by simple binary rules; instead, the best model for the data was a linear regression fit of a quantitative measure of gene activity to multiple features of the regulatory sequence.

Ether↗

PubMed2002

Generation of amplifiable genome-specific oligonucleotide probes and libraries.

Here we describe a process for the generation of oligonucleotide libraries representative of a given nucleic acid. Starting from at random pool of DNA oligonucleotides, the technique selects only those that hybridize to the nucleic acid template. This selection yields a highly specific library that represents an oligonucleotide image of the chosen template. The novel quality of this approach is the generation of amplifiable oligonucleotide probes that are of unique length and are easily subjected to differential selection. Here we apply this technique to produce different genomic oligonucleotide libraries and show that these genomic oligonucleotide libraries do not cross-hybridize. Differential selection of these genomic oligonucleotide libraries produces oligonucleotides that can be used in the identification, characterzation, and isolation of nucleic acids.

Adenoviridae↗

PubMed2003

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

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

Bacterial Proteins↗

PubMed2003

Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.

The normalization and subtraction of highly expressed cDNAs from relatively large tissues before cloning dramatically enhanced the gene discovery by sequencing for the mouse full-length cDNA encyclopedia, but these methods have not been suitable for limited RNA materials. To normalize and subtract full-length cDNA libraries derived from limited quantities of total RNA, here we report a method to subtract plasmid libraries excised from size-unbiased amplified lambda phage cDNA libraries that avoids heavily biasing steps such as PCR and plasmid library amplification. The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization.

Gene Expression Profiling↗

PubMed2006

The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.).

The narrow-leafed lupin possesses valuable traits for environment-friendly agriculture and for the production of unconventional agricultural products. Despite various genetic and environmental studies, the breeding of improved cultivars has been slow due to the limited knowledge of its genomic structure. Further advances in genomics require, among other things, the availability of a genomic DNA library with large inserts. We report here on the construction of the first DNA library cloned in a BAC (bacterial artificial chromosome) vector from diploid Lupinus angustifolius L. cv. Sonet. The high molecular weight DNA used for its preparation was isolated from interphase nuclei that were purified by flow cytometry. The library comprises 55,296 clones and is ordered in 144x384-well microtitre plates. With an average insert size of 100 kb, the library represents six haploid genome equivalents. Thanks to the purification of the nuclei by flow cytometry, contamination with chloroplast DNA and mitochondrial DNA was negligible. The availability of a BAC library opens avenues for the development of a physical contig map and positional gene cloning, as well as for the analysis of the plant's genome structure and evolution.

Chromosomes, Artificial, Bacterial↗

PubMed2005

Screening for PreS specific binding ligands with a phage displayed peptides library.

AIM: To construct a random peptide phage display library and search for peptides that specifically bind to the PreS region of hepatitis B virus (HBV). METHODS: A phage display vector, pFuse8, based on the gene 8 product (pVIII) of M13 phage was made and used to construct a random peptide library. E.coli derived thioredoxin-PreS was purified with Thio-bond beads, and exploited as the bait protein for library screening. Five rounds of bio-panning were performed. The PreS-binding specificities of enriched phages were characterized with phage ELISA assay. RESULTS: A phage display vector was successfully constructed as demonstrated to present a pVIII fused HBV PreS1 epitope on the phage surface with a high efficiency. A cysteine confined random peptide library was constructed containing independent clones exceeding 5+/-10(8) clone forming unit (CFU). A pool of phages showing a PreS-binding specificity was obtained after the screening against thio-PreS with an enrichment of approximately 400 times. Five phages with high PreS-binding specificities were selected and characterized. Sequences of the peptides displayed on these phages were determined. CONCLUSION: A phage library has been constructed, with random peptides displaying as pVIII-fusion proteins. Specific PreS-binding peptides have been obtained, which may be useful for developing antivirals against HBV infection.

Amino Acid Sequence↗

PubMed2002

Construction of cDNA representational difference analysis based on two cDNA libraries and identification of garlic inducible expression genes in human gastric cancer cells.

AIM: To elucidate molecular mechanism of chemopreventive efficacies of garlic against human gastric cancer (HGC). METHODS: HGC cell line BGC823 was treated with Allitridi (a kind of garlic extract) and Allitridi-treated and parental BGC823 cDNA libraries were constructed respectively by using lambdaZAP II vector. cDNA Representational Difference Analysis (cDNA RDA) was performed using Bam H I cutting-site and abundant cDNA messages provided by the libraries. Northern blot analysis was applied to identify the obtained difference products. RESULTS: Two specific cDNA fragments were obtained and characterized to be derived from homo sapiens folate receptor alpha (FRalpha) gene and calcyclin gene respectively. Northern blot results showed a 4-fold increase in FRalpha gene expression level and 9-fold increase in calcyclin mRNA level in BGC823 cells after Allitridi treatment for 72h. CONCLUSION: The method of cDNA RDA based on cDNA libraries combines the high specificity of cDNA RDA with abundant cDNA messages in cDNA library; this expands the application of cDNA library and increases the specificity of cDNA RDA. Up-regulation of FRalpha gene and calcyclin gene expressions induced by Allitridi provide valuable molecular evidence for the efficacy garlic in treating HGC as well as other diseases.

Allyl Compounds↗

PubMed2006

Korean BAC library construction and characterization of HLA-DRA, HLA-DRB3.

A human bacterial artificial chromosome (BAC) library was constructed with high molecular weight DNA extracted from the blood of a male Korean. This Korean BAC library contains 100,224 clones of insert size ranging from 70 to 150 kb, with an average size of 86 kb, corresponding to a 2.9-fold redundancy of the genome. The average insert size was determined from 288 randomly selected BAC clones that were well distributed among all the chromosomes. We developed a pooling system and three-step PCR screen for the Korean BAC library to isolate desired BAC clones, and we confirmed its utility using primer pairs designed for one of the clones. The Korean BAC library and screening pools will allow PCR-based screening of the Korean genome for any gene of interest. We also determined the allele types of HLA-DRA and HLA-DRB3 of clone KB55453, located in the HLA class II region on chromosome 6p21.3. The HLA-DRA and DRB3 genes in this clone were identified as the DRA*010202 and DRB3*01010201 types, respectively. The haplotype found in this library will provide useful information in future human disease studies.

Asian People↗

PubMed1996

What nurses think of library services: a research study.

The need for more research in nursing has been highlighted by many organisations and official bodies. However, there is evidence to suggest that many nurses involved in research are reluctant to use libraries. This study aimed to ascertain the attitudes of nursing researchers towards libraries by means of questionnaires and interviews. A five-page questionnaire was sent to 289 nursing researchers throughout the UK in July 1994. Common problems found by the researchers were lack of time to get to the library (67 per cent), the library not having the information required (60 per cent) and the library being too far away (40 per cent). The author suggests that nurses and researchers should work more in co-operation with the librarian.

Attitude of Health Personnel↗

PubMed1995

Enhancing library services: an exploration in meeting customer needs through total quality management.

Total Quality Management (TQM) is a process which focuses on understanding customer needs and improving customer service and satisfaction. A TQM committee was created at the Devereux Foundation's Professional Library to assess user satisfaction and make recommendations for improving library services to better meet consumer needs. The committee distributed a satisfaction survey to 156 of the most likely library users and 84 (54%) were returned. Overall, survey results indicate that most consumers are satisfied with the materials and services provided by the Professional Library. Recommendations for improving library services and strategies for implementing these recommendations are discussed.

Consumer Behavior↗

PubMed1988

Quality assurance: establishing a program for libraries.

"Quality Assurance" (QA) is a practical tool for library management, a link in the library's relationship with administrative decision makers. Instituting or refining a QA program takes into account formal and informal methods. Described are one library's program and problem-solving model, the role of others in the library's program, types of recordkeeping, and integration of the library program with organizational QA. Positive results include participation in management-level activities and improvement in quality and delivery of services and products. Ten suggestions are made to begin a QA program.

Hospital Bed Capacity, 300 to 499↗

PubMed1999

Protective immune responses induced by vaccination with an expression genomic library of Leishmania major.

To develop an effective vaccine against the intracellular protozoan parasite Leishmania spp., we investigated the feasibility of expression library immunization (ELI) in the mouse. Genomic expression libraries of L. major were constructed and used to immunize mice. One of the three libraries (L1, with 10(5) clones) induced a significant protective immune response and delayed the onset of lesion development in highly susceptible BALB/c mice after i.m. immunization, compared with control mice immunized with the empty vector (EV). L1 was then divided into five sublibraries of approximately 2 x 10(4) clones each. Mice immunized with one of the sublibraries (SL1A) developed an even stronger protective effect than that induced by L1. SL1A was further divided into 20 sublibraries (SL2) of approximately 10(3) clones each. One of the SL2 libraries (SL2G) induced a strong protective effect against L. major infection. In direct comparative studies, the protective effect of the sublibraries was in the order of SL2G > SL1A > L1. Lymphoid cells from mice vaccinated with SL2G produced more IFN-gamma and NO, compared with cells from control mice injected with EV. Serum from the vaccinated mice also contained more parasite-specific IgG2a Ab, compared with controls. Therefore, these data demonstrate that ELI is feasible against this complex intracellular parasitic infection, by preferentially inducing the development of Th1 responses. Furthermore, by sequential division of the libraries, this approach may be used to enrich and identify protective genes for effective gene vaccination against other parasitic infections.

Animals↗

PubMed1999

Development of a hyperimmune anti-MUC-1 single chain antibody fragments phage display library for targeting breast cancer.

Radioimmunotherapy (RIT) has demonstrated potential for improving clinical cancer therapy. Optimizing the approach has proven difficult thus far. Antibody phage display libraries provide unique molecules that could improve RIT. A phage display library of single chain antibody fragments (scFv) against the MUC-1 mucin molecule, which is expressed on 90% of human breast cancers, was produced from the spleen cells of MUC-1 hyperimmunized BALB/c mice. Increased serum IgG levels, 15 times baseline, were detected following the third immunization. RNA from the spleen cells was isolated, cDNA was made, and variable heavy and variable light immunoglobulin chain gene regions were amplified using PCR technology. The variable heavy and variable light chain gene regions were combined with a flexible linker, ligated into the pCANTAB 5E phagemid vector, and electroporated into TG1 Escherichia coli cells. A library of 10(7) initial colonies was compiled. Forty-six of 288 colonies screened for reactivity demonstrated binding to MUC-1-expressing MCF-7 breast cancer cell membrane fragments. Anti-MUC-1 library diversity evaluated by BstNI digest demonstrated that 52% of the anti-MUC-1 scFv binding MCF-7 possessed individual banding patterns representative of approximately 5 x 10(5) colonies likely able to recognize distinct epitopes present on MUC-1 positive human breast cancers. In summary, the anti-MUC-1 scFv antibody phage library contains diverse scFv molecules, which should provide unique characteristics and epitope recognition. These molecules will be used in the development of pretargeting RIT strategies designed to improve the clinical outcome of patients with breast cancer.

Animals↗

PubMed1999

Antibody phage libraries for the next generation of tumor targeting radioimmunotherapeutics.

Pretargeting techniques have shown promise for enhancement of the therapeutic index of radioimmunotherapy for cancer. However, methods to vary and compare antibody configurations and select optimal combinations have proved rather formidable. New options for the construction of pretargeting molecules are provided by sophisticated use of the diversity and malleability of antibody genes. Diverse arrays of single-chain antibody fragments (scFvs) can now be obtained reactive with virtually any target antigen by selection from human naive phage antibody libraries. ScFvs can also be cloned directly from hybridoma for construction of phage libraries that facilitate subsequent manipulation: e.g., affinity maturation and modification of specificity. ScFvs affinity selected from these sources to their specific antigen targets have demonstrated a wide spectrum of binding characteristics. ScFvs selected from a large human naive phage antibody library by binding Cu-1,4,8,11-tetra-azacyclotetradecane-N,N',N'',N'''-tetraacetic acid (TETA) or Y-1,4,7,10-tetra-azacyclododecane-N,N',N'',N'''-tetraacetic acid (DOTA) have shown diversity by DNA fingerprints. DNA sequence information confirmed that the anti-TETA scFv represented diverse scFv gene families. ScFvs for Y-DOTA and those for lymphoma-associated HLA DR10 (Lym-1) were selected in a similar manner from mouse antibody gene libraries derived from hybridoma. ScFv clones for each of these antigens were chosen for further study based on the results of ELISA assays involving the respective cell membrane or metal chelate antigens. A PCR primer system built to pCANTAB 5E expression vector sequence was designed to facilitate cloning of antibody heavy (V(H)) and light (V(L)) genes from selected scFvs as cassettes into diabody modules. Thus, chosen scFvs could be expressed in the same diabody format for comparative study. Selected mouse anti-DOTA scFv and Lym-1 scFv genes were linked as V(HA) anti-DOTA-link-V(LB) Lym-1; V(HB) anti-DOTA-link-V(LA) Lym-1 and ligated into the pCANTAB 5E vector. Corresponding diabodies were expressed in Escherichia coli and purified by affinity chromatography. Here we provide a perspective on the power of antibody phage libraries and the possibilities of creating simple molecular formats that can be used en route to the development of new tumor targeting and pretargeting molecules.

Animals↗