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Making antibody fragments using phage display libraries.

To by-pass hybridoma technology and animal immunization, we are trying to build antibodies in bacteria by mimicking features of immune selection. Recently we used fd phage to display antibody fragments fused to a minor coat protein, allowing enrichment of phage with antigen. Using a random combinatorial library of the rearranged heavy (VH) and kappa (V kappa) light chains from mice immune to the hapten 2-phenyloxazol-5-one (phOx), we have now displayed diverse libraries of antibody fragments on the surface of fd phage. After a single pass over a hapten affinity column, fd phage with a range of phOx binding activities were detected, at least one with high affinity (dissociation constant, Kd = 10(-8) M). A second pass enriched for the strong binders at the expense of the weak. The binders were encoded by V genes similar to those found in anti-phOx hybridomas but in promiscuous combinations (where the same V gene is found with several different partners). By combining a promiscuous VH or V kappa gene with diverse repertoires of partners to create hierarchical libraries, we elicited many more pairings with strong binding activities. Phage display offers new ways of making antibodies from V-gene libraries, altering V-domain pairings and selecting for antibodies with good affinities.

Amino Acid Sequence↗

Protection against mycoplasma infection using expression-library immunization.

As is evident from the human immunodeficiency virus epidemic, there is no systematic method for producing a vaccine. Genetic immunization is a new approach to vaccine production that has many of the advantages of live/attenuated pathogens but no risk of infection. It involves introducing DNA encoding a pathogen protein into host cells and has shown promise in several disease models. Here we describe a new method for vaccine development, expression-library immunization, which makes use of the technique of genetic immunization and the fact that all the antigens of a pathogen are encoded in its DNA. An expression library of pathogen DNA is used to immunize a host thereby producing the effects of antigen presentation of a live vaccine without the risk. We show that even partial expression libraries made from the DNA of Mycoplasma pulmonis, a natural pathogen in rodents, provide protection against challenge from the pathogen. Expression library immunization may prove to be a general method for vaccination against any pathogen.

Animals↗

Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display.

Here we applied ribosome display to in vitro selection and evolution of single-chain antibody fragments (scFvs) from a large synthetic library (Human Combinatorial Antibody Library; HuCAL) against bovine insulin. In three independent ribosome display experiments different clusters of closely related scFvs were selected, all of which bound the antigen with high affinity and specificity. All selected scFvs had affinity-matured up to 40-fold compared to their HuCAL progenitors, by accumulating point mutations during the ribosome display cycles. The dissociation constants of the isolated scFvs were as low as 82 pM, which validates the design of the naïve library and the power of this evolutionary method. We have thus mimicked the process of antibody generation and affinity maturation with a synthetic library in a cell-free system in just a few days, obtaining molecules with higher affinities than most natural antibodies.

Amino Acid Sequence↗

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

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.

Apoptosis↗

Affinity-based screening of combinatorial libraries using automated, serial-column chromatography.

We have developed an automated serial chromatographic technique for screening a library of compounds based upon their relative affinity for a target molecule. A "target" column containing the immobilized target molecule is set in tandem with a reversed-phase column. A combinatorial peptide library is injected onto the target column. The target-bound peptides are eluted from the first column and transferred automatically to the reversed-phase column. The target-specific peptide peaks from the reversed-phase column are identified and sequenced. Using a monoclonal antibody (3E-7) against beta-endorphin as a target, we selected a single peptide with sequence YGGFL from approximately 5800 peptides present in a combinatorial library. We demonstrated the applicability of the technology towards selection of peptides with predetermined affinity for bacterial lipopolysaccharide (LPS, endotoxin). We expect that this technology will have broad applications for high throughout screening of chemical libraries or natural product extracts.

Amino Acid Sequence↗

A DNA transformation-competent Arabidopsis genomic library in Agrobacterium.

We have constructed a nuclear genomic library from the cruciferous plant Arabidopsis thaliana ecotype Columbia in a cosmid vector, pLZO3, and a host organism, Agrobacterium tumefaciens AGL1, which can directly DNA-transform the parent organism, Arabidopsis. The broad host range cosmid pLZO3 carries a gentamicin acetyltransferase gene as bacterial selective marker and tandem, chimeric neomycin and streptomycin phosphotransferase genes as plant selective markers. Agrobacterium AGL1 carries the hypervirulent, attenuated tumor-inducing plasmid pTiBo542 from which T-region DNA sequences have been precisely deleted, allowing optimal DNA transformation of many dicotyledonous plants. Agrobacterium AGL1 also carries an insertion mutation in its recA general recombination gene, which stabilizes the recombinant plasmids. The Arabidopsis genomic library consists of some 21,600 clones gridded onto 96-well microtiter dishes and, if random, carries at least three genomic equivalents. When probed for the presence of several Arabidopsis low copy-number genes, the genomic library seems representative. As with the unicellular organisms Escherichia coli and Saccharomyces cerevisiae, this DNA transformation competent genomic library should expedite gene isolation, by gene rescue, in multicellular organisms like Arabidopsis.

Agrobacterium tumefaciens↗

Construction of a mouse yeast artificial chromosome library in a recombination-deficient strain of yeast.

We have constructed a new generation yeast artificial chromosome (YAC) library from female C57BL/10 mice in a recombination-deficient strain of Saccharomyces cerevisiae carrying a mutation in the RAD52 gene. The YAC library contains 41,568 clones with an average insert size of 240 kilobases, representing a greater than threefold coverage of the mouse genome. Currently, the library can be screened by polymerase chain reaction and we have isolated positive clones at a number of loci in the mouse genome. This rad52 library should enable a long-term assessment of the effect of one of the yeast recombination pathway genes on both, genome-wide YAC clone stability and the frequency of chimaeric clones.

Animals↗

A comprehensive library of fluorescent transcriptional reporters for Escherichia coli.

E. coli is widely used for systems biology research; there exists a need, however, for tools that can be used to accurately and comprehensively measure expression dynamics in individual living cells. To address this we present a library of transcriptional fusions of gfp to each of about 2,000 different promoters in E. coli K12, covering the great majority of the promoters in the organism. Each promoter fusion is expressed from a low-copy plasmid. We demonstrate that this library can be used to obtain highly accurate dynamic measurements of promoter activity on a genomic scale, in a glucose-lactose diauxic shift experiment. The library allowed detection of about 80 previously uncharacterized transcription units in E. coli, including putative internal promoters within previously known operons, such as the lac operon. This library can serve as a tool for accurate, high-resolution analysis of transcription networks in living E. coli cells.

Escherichia coli↗

Mapping epitopes of neutralizing monoclonal antibodies using phage random peptide libraries.

Identification of protective determinants from microbial proteins is a necessary step in the rational design of subunit vaccines. We have previously used a synthetic peptide scan (Pepscan) assay to map a panel of eight neutralizing monoclonal antibodies (mAb; designated as C1.1 to C1.8) to a common motif sequence from Chlamydia trachomatis. In the present study, five of the eight mAbs were used to screen phage random peptide libraries. mAbs C1.1 and C1.3 selected a motif sequence of G-L-X-N-D from a pIII-based phage random peptide library and a motif sequence of G-X-X-N-D from a pVIII-based random peptide library while mAbs C1.6 to C1.8 failed to select recognizable motifs from either of the phage libraries. However, C1.6 to C1.8 bound to the same motif sequence displayed on phage when the appropriate conformational constraints were imposed onto the motif sequence. Thus the specificity of the mAbs identified on Pepscan assays correlates with the mAbs' dependence on local epitope constraints displayed on the phage surface.

Amino Acid Sequence↗

Topochemical exploration of potent compounds using retro-enantiomer libraries of cyclic pentapeptides.

Cyclic pentapeptides have been adopted as conformationally restricted peptide templates to dispose pharmacophores of bioactive peptides. In our recent study, use of two orthogonal cyclic pentapeptide libraries involving conformation-based and sequence-based libraries containing critical residues of a bioactive peptide led to the discovery of potent downsized peptides that possess activity comparable to that of the parent peptide. The present study demonstrates that a third library consisting of retro-enantiomers (retro-inverso peptides) that possess not only all residues with the opposite configuration to those in the corresponding original peptide but also amino acid sequences with reversed arrangement, is important as an alternative library for rationally finding active compounds.

Amino Acid Sequence↗

Optimized protocols for the isolation of specific protein-binding peptides or peptoids from combinatorial libraries displayed on beads.

Many methods have been published by which combinatorial libraries may be screened for compounds capable of manipulating the function(s) of a target protein. One of the simplest approaches is to identify compounds in a library that bind the protein of interest, since these binding events usually occur on functionally important surfaces of the protein. These protein-binding compounds could also be of utility as protein capture agents in the construction of protein-detecting microarrays or related analytical devices and as reagents for the affinity purification of proteins from complex mixtures. In this article, we provide optimized methods for screening libraries of molecules displayed on the beads on which they were synthesized. This is a particularly convenient format for library screening for laboratories with limited budgets and modest robotics capabilities.

Chalcone↗

Action of a library of O-glycosylation inhibitors on the growth of human colorectal cancer cells in culture.

O-glycosylation is thought to play a significant role in the regulation of cell growth. However, only limited information is available, and few specific and selective inhibitors have been found. We have synthesized a library of O-glycosylation inhibitors based on benzyl-O-N-acetyl-D-galactosamine. These inhibitors were tested with an established series of human colorectal cancer cell lines, which model the adenoma-carcinoma sequence. Cancer cells were incubated with the inhibitors, and examined for cell growth patterns, and cellular and subcellular glycosylation using a range of lectins with confocal microscopy. The specificity of O-glycan inhibition was confirmed for the library, relative to other forms of glycosylation. All inhibitors tested resulted in smaller cell yields. However, a differential effect on O-glycosylation was detected using the lectins showing variation of localization at a subcellular level in the various cell lines. Further differential action of the inhibitor library was observed for apoptosis and on the cell cycle with the cell lines tested. This work demonstrates that O-glycosylation is closely involved in the regulation of cell growth in colorectal cancer cells and that the generation of a library of low-molecular-mass inhibitors offers a valuable means of examining this regulation at the molecular level.

Cell Division↗

Planning a new medical library: a personal perspective and review of the literature.

Principles of library planning and a review of the literature in relation to the planning of a new library for the Royal College of Surgeons in Ireland are discussed. The role of the Librarian with regard to planning, the importance of the Library brief, the impact of technology on library buildings, and the provision of adequate accommodation for collections, readers and staff are considered.

Facility Design and Construction↗

Management by agreement: contracting for library services in South West Thames.

On 1 April 1991, the financial base of the NHS underwent its most dramatic change since its inception in 1948. All NHS services are now based on contracts and this has major implications for library services. This change was perceived by the South West Thames Regional Library Service as presenting a unique opportunity and the paper outlines the background to the thinking and the strategy adopted to meet the challenges. Sources of library funding and precise spending details were identified by means of a survey and contracts agreed covering all NHS staff in each of the 13 districts. The contracts are operating as 'shadow contracts' for 1991-92 allowing a valuable period of evaluation and monitoring before any money actually changes hands. The survey form for collecting library budgetary information and the service agreement are included as Appendices to the article.

Budgets↗

Libraries and the R&D strategy: a way forward.

As guest editor for the December 1994 issue of Health Libraries Review, I chose the theme of Evidence-Based Practice. In my editorial I suggested that Evidence-based Practice offered tremendous opportunities for NHS librarians to demonstrate their skills in supporting a knowledge-based NHS, because many clinicians had complained that they did not have time, retrieval skills of knowledge of relevant information resources to be effective at finding scientific evidence. Librarians, on the other hand have advanced online searching skills, rapid document retrieval and delivery services, and up-to-date knowledge of the world's medical information resources and networks. These skills mean that librarians are not only well-placed to support clinicians in finding and sifting scientific evidence, but also in teaching clinicians how to search for and store information themselves. NHS librarians have not been slow to recognize these opportunities and innovative professional development programmes have appeared to help hone their skills, such as the Librarian of the 21st Century Programme in the Anglia and Oxford region. The success of NHS librarians in supporting evidence-based health care has led to their formal development in evidence-based medicine workshops for clinicians in a number of regions. In March 1996, as NHS Library Adviser. I was asked to prepare a paper for the R&D Board of the NHS Executive about how this library support could be formally integrated into the R&D Strategy. My paper was unanimously endorsed by the Board and later by the Central R&D Committee of the NHS Executive. It suggests principles of library provision in support of R&D and is reprinted below.

Databases, Factual↗

A Delphi survey of research priorities and identified areas for collaborative research in health sector library and information services UK.

The survey aims were to determine research priorities in the Health Library and Information Services sector in the United Kingdom as to their perceived value for the professional and impact on user needs and to identify areas suitable for collaborative research. A 34-member panel consisting of the Chairs of professional groups, journal editors, educationalists, key organizations and representatives from the Health Libraries Group, Libraries for Nursing and University Health Science Libraries professional groups, participated in a three-round postal questionnaire survey using the Delphi Technique. Consensus was achieved for a final set of 20 research priorities. The priorities and their category groups are discussed in the context of (i) the current R&D scene, and (ii) the health information environment. Six developmental recommendations are provided.

Cooperative Behavior↗

Opportunities on the Web: a role for information professionals, using the development of the BMA Library Online Service as a case study.

The paper considers how attributes and skills fundamental to the information profession may be applied to the development and management of Web-based services and resources. It also looks at the need for the acquisition of new skills as part of a continuing professional development programme. The report considers the changing role of the Webmaster and the implications this might have in terms of the role of information professionals. To offer a practical example, from within the healthcare sector, the article goes on to describe the development of BMA Library Online. This is the BMA Library's own suite of Web-based information services and resources for personal members, institutional members and staff. The library's own Web team has been responsible for the development and maintenance of BMA Library Online. To conclude, the paper looks forward to future possibilities for information professionals as Web developers and at how this might be influenced by changes in the Webmaster role. It is crucial that skills and expertise are shared as the roles that go to make up a Webmaster or Webmaster team continue to merge and evolve, and with the possible wider distribution of provision of Web content within organizations.

Information Management↗

A first class knowledge service: developing the National electronic Library for Health.

With the introduction of clinical governance and the move towards evidence-based practice, there is a growing need to provide health professionals and patients, and the public, with high quality information. Developments in the health service have added weight and urgency to this need. The National electronic Library for Health (NeLH) has a key role to play in providing health professionals with a core knowledge base of accredited and evaluated information. The Pilot NeLH was launched in November and this article outlines the progress and achievements made during this time. The NeLH is based around a central website featuring core resources and links to commissioned specialist collections. Over 70 information resources, including bibliographic databases and full text publications, are accessible via the NeLH, which aims to act as a one-stop shop to support evidence-based decision-making. Much work has been undertaken on national procurement and licensing, particularly in partnership with National Health Service (NHS) libraries. Partnerships as a whole are crucial to ensure true seamless access for health professionals. Key partners include NHS libraries, NHS Direct Online and the electronic Library for Social Care. A short glossary is included for those readers less familiar with current health service developments in the UK.

Cooperative Behavior↗