Removing the redundancy from randomised gene libraries

Amino acid substitution plays a vital role in both the molecular engineering of proteins and analysis of structure-activity relationships. High-throughput substitution is achieved by codon randomisation, which generates a library of mutants (a randomised gene library) in a single experiment. For full randomisation, key codons are typically replaced with NNN (64 sequences) or NNG CorT (32 sequences). This obligates cloning of redundant codons alongside those required to encode the 20 amino acids. As the number of randomised codons increases, there is therefore a progressive loss of randomisation efficiency; the number of genes required per protein rises exponentially. The redundant codons cause amino acids to be represented unevenly; for example, methionine is encoded just once within NNN, whilst arginine is encoded six times. Finally, the organisation of the genetic code makes it impossible to encode functional subsets of amino acids (e.g. polar residues only) in a single experiment. Here, we present a novel solution to randomisation where genetic redundancy is eliminated; the number of different genes equals the number of encoded proteins, regardless of codon number. There is no inherent amino acid bias and any required subset of amino acids may be encoded in one experiment. This generic approach should be widely applicable in studies involving randomisation of proteins. © 2003 Elsevier Ltd. All rights reserved.

A new randomization assay reveals Unexpected elements of sequence bias in model 'randomized' gene libraries:Implications for biopanning

Although techniques such as biopanning rely heavily upon the screening of randomized gene libraries, there is surprisingly little information available on the construction of those libraries. In general, it is based on the cloning of 'randomized' synthetic oligonucleotides, in which given position(s) contain an equal mixture of all four bases. Yet, many supposedly 'randomized' libraries contain significant elements of bias and/or omission. Here, we report the development and validation of a new, PCR-based assay that enables rapid examination of library composition both prior to and after cloning. By using our assay to analyse model libraries, we demonstrate that the cloning of a given distribution of sequences does not necessarily result in a similarly composed library of clones. Thus, while bias in randomized synthetic oligonucleotide mixtures can be virtually eliminated by using unequal ratios of the four phosphoramidites, the use of such mixtures does not ensure retrieval of a truly randomized library. We propose that in the absence of a technique to control cloning frequencies, the ability to analyse the composition of libraries after cloning will enhance significantly the quality of information derived from those libraries. (C) 2000 Published by Elsevier Science B.V. All rights reserved.

Public libraries, citizens and the post democracy

This essay explores the relationship between the development of public libraries in the context of an increasingly market-dominated economy and marketised society. It argues that although neo-liberalism as a policy goal and practice has taken different forms over time, there are common themes in terms of its emphasis on market values, privatisation, and the support of measures that reduce the role of public funding and the state in the provision of public services. This has led some commentators to express concerns that the meaning and practice of citizenship and democracy is being transformed, managed or otherwise diminished. These concerns are compounded by changes effected by new digital technology. Imbricated with this issue are debates surrounding the future of the public library, and attempts by librarians and others to reinvent and reimagine its purpose. With reference to some innovative initiatives in the USA and Scandinavia, it is suggested that public libraries, through their service and spatial rearticulation, can conceivably help strengthen and revitalise public democracy and the public sphere.

Increased diversity of libraries from libraries: chemoinformatic analysis of bis-diazacyclic libraries

Combinatorial libraries continue to play a key role in drug discovery. To increase structural diversity, several experimental methods have been developed. However, limited efforts have been performed so far to quantify the diversity of the broadly used diversity-oriented synthetic (DOS) libraries. Herein we report a comprehensive characterization of 15 bis-diazacyclic combinatorial libraries obtained through libraries from libraries, which is a DOS approach. Using MACCS keys, radial and different pharmacophoric fingerprints as well as six molecular properties, it was demonstrated the increased structural and property diversity of the libraries from libraries over the individual libraries. Comparison of the libraries to existing drugs, NCI Diversity and the Molecular Libraries Small Molecule Repository revealed the structural uniqueness of the combinatorial libraries (mean similarity < 0.5 for any fingerprint representation). In particular, bis-cyclic thiourea libraries were the most structurally dissimilar to drugs retaining drug-like character in property space. This study represents the first comprehensive quantification of the diversity of libraries from libraries providing a solid quantitative approach to compare and contrast the diversity of DOS libraries with existing drugs or any other compound collection.

Novel anti-bacterials against MRSA:Synthesis of focussed combinatorial libraries of tri-substituted 2(5H)-furanones

Mucobromic and mucochloric acid were used as building blocks for the construction of a chemical combinatorial library of 3,4,5-trisubstituted 2(5H)-furanones. With these 2 butenolide building blocks, and eight alcohols a sublibrary of 16 dihalogenated 5-alkoxy-2(5H)-furanones was prepared. This sublibrary of 5-alkoxylated furanones was reacted with 16 amines generating a full size focussed combinatorial library of 256 individual compounds. This three dimensional combinatorial library of 3-halogen-4-amino-5-alkoxy-2(5H)-furanones was prepared around the benzimidazolyl furanone lead structure by applying a solution phase combinatorial chemistry concept. Typical representatives of the library were purified and fully characterized and one x-ray structures was recorded, additionally. The 3-bromo-4-benzimizazolyl-5-methoxy-2(5H)furanone, Br-A-l, showed an MIC of 8 μg/ml against the multiresistant Staphylococcus aureus ( MRSA). © 2006 Bentham Science Publishers Ltd.

Public libraries and the right to the [smart] city

The future of public libraries has been threatened by funding cuts and new digital technologies which have led many people to question their traditional role and purpose. However, freedom of information, ready access to knowledge and information literacy in all its digital and analog guises are more important than ever. Thus, public libraries remain significant spaces and places where people can socially interact and learn. In many countries public libraries are reinventing themselves and part of this process has been the redesign of library services and the design and construction of new library building and facilities that articulate the values, purpose and role of what has been termed 'the next library'. Following discussion of new library developments in London, Birmingham and Worcester in the UK, Aarhus in Denmark and Helsinki in Finland, the article concludes that public libraries are now both social and media spaces as well as being important physical places that can help city dwellers decide what type of urban world they want to see.

Intellectual Communications and Contemporarly Technologies Alternatives of the Science Libraries

(Summary of: Varbanova-Dencheva, K. Intellectual communications and contemporarly technologies. Alternatives of the science libraries. Sofia, Marin Drinov academic publishing house. 2003, 114p. ) The new technologies and the globalization are the factors which have brought essential changes in human society and its environment. The unceasing dynamic changes imposed new strategies for survival and prosperity of institutions and people in the new conditions. The spheres with greatest potential for achieving competition priority are compatible to the fastness of research results implementation in each field of human activity. The extended knowledge requires narrower specialization as well as interdisciplinarity to solve the arising problems. The new research fields and trends are a synthesis of science and high technologies determined by the new discoveries. The present study aims at finding answers to the questions about the place of science library in the dynamic restructuring of research environment. The necessity of transformation of the scientific library’s genetically set functions from a guardian of the achieved knowledge to an active participant in the creation of new knowledge is a natural consequence of the processes and tendencies of the social medium. The priorities of Europe and USA for intensive creation of knowledge economics are at the first place and this requires intensification of that research an integral part of which are the new communications realized at a new technological level.

Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity.

Photographic Plate Libraries at European Astronomical Observatories

ACM Computing Classification System (1998): J.2.

Survey of Existing Services in the Mathematical Digital Libraries and Repositories in the EuDML Project

This paper presents a survey of the existing services provided by the digital libraries and repositories on mathematics of the content provider partners in the EuDML project. The purpose is to support the development of the concepts, criteria and methods for the continuous evaluation of these and new relevant existing services. The work was concentrated on the classification of the relevant services in order to specify a common evaluating structure.

Digitization of Literary Heritage in the Bulgarian Libraries: Facing Problems and Challenges

Paper deals with the current issues and challenges before digitization of literary heritage in the Bulgarian libraries. Main problems are outlined. Socialization of digitized heritage is commented.

Digital Libraries and Portals Saving National Cultural Heritage (IMI–BAS Experience)

The current research activities of the Institute of Mathematics and Informatics at the Bulgarian Academy of Sciences (IMI—BAS) include the study and application of knowledge-based methods for the creation, integration and development of multimedia digital libraries with applications in cultural heritage. This report presents IMI-BAS’s developments at the digital library management systems and portals, i.e. the Bulgarian Iconographical Digital Library, the Bulgarian Folklore Digital Library and the Bulgarian Folklore Artery, etc. developed during the several national and international projects: - "Digital Libraries with Multimedia Content and its Application in Bulgarian Cultural Heritage" (contract 8/21.07.2005 between the IMI–BAS, and the State Agency for Information Technologies and Communications; - FP6/IST/P-027451 PROJECT LOGOS "Knowledge-on-Demand for Ubiquitous Learning", EU FP6, IST, Priority 2.4.13 "Strengthening the Integration of the ICT research effort in an Enlarged Europe" - NSF project D-002-189 SINUS "Semantic Technologies for Web Services and Technology Enhanced Learning". - NSF project IO-03-03/2006 ―Development of Digital Libraries and Information Portal with Virtual Exposition "Bulgarian Folklore Heritage". The presented prototypes aims to provide flexible and effective access to the multimedia presentation of the cultural heritage artefacts and collections, maintaining different forms and format of the digitized information content and rich functionality for interaction. The developments are a result of long- standing interests and work in the technological developments in information systems, knowledge processing and content management systems. The current research activities aims at creating innovative solutions for assembling multimedia digital libraries for collaborative use in specific cultural heritage context, maintaining their semantic interoperability and creating new services for dynamic aggregation of their resources, access improvement, personification, intelligent curation of content, and content protection. The investigations are directed towards the development of distributed tools for aggregating heterogeneous content and ensuring semantic compatibility with the European digital library EUROPEANA, thus providing possibilities for pan- European access to rich digitalised collections of Bulgarian cultural heritage.

Workshop: E-Books and e-Lending in Libraries – Challenges and Opportunities

The proposed event is part of the 2013 program of IFLA (International Federation of Library Association) as well IFLA – CLM Committee on eBooks and e-lending. The proposed event is also part of the activities of a research project with international participation "Copyright Policies of libraries and other cultural institutions” (2012-2014), (financed by National Science Fund of the Bulgarian Ministry of Education, Youth and Science, Contract No ДФНИ-К01/0002-21.11.2012).