“Shotgun” cloning of skin peptide precursors from skin secretion-derived cDNA libraries of the Fujian large-headed frog, Limnonectes fujianensis

Amphibian skin secretions are rich sources of biologically-active peptides and several studies involving molecular cloning of their biosynthetic precursors have revealed that many exhibit highly-conserved domain architectures with an associated high degree of primary structural conservation of the signal peptides. This conservation of primary structure is reflected at the level of nucleotide sequence — a finding that has permitted our group to design primers to these sites facilitating “shotgun” cloning using cDNA libraries from uninvestigated species. Here we describe the results of such an approach using a skin secretion-derived cDNA library from the Fujian large-headed frog, Limnonectes fujianensis, a completely unstudied species. In over 50 clones studied by this approach, 12 were found to encode peptides of different primary structure. Representatives of 5 different families of antimicrobial peptides derived from the skins of ranid frogs were found and these were brevinin-1 (n = 3), the ranatuerin-2 (n = 3), esculentin-2 (n = 1), temporin (n = 1) and chensinin (n = 1). Three clones encoded peptides that were novel with no homologues present in contemporary on-line databases. These included two related 16-mer peptides, named peptides SC-16a and b, and an unrelated 24-mer, named peptide AG-24. Preliminary biological characterisation of SC-16a has demonstrated an antimicrobial activity against Gram-negative bacteria with a minimal inhibitory concentration of 35 µM with no observable haemolysis up to 200 µM. This finding may suggest that this peptide represents a novel class of antimicrobial with little effect on eukaryotic membranes.

Construction of cDNA libraries from trifluoroacetic acid-solvated amphibian skin secretions: molecular cloning of multiple bombinin-like peptide precursor transcripts from a library of yellow-bellied toad (Bombina variegata) secretion

Amphibian skin secretions are renowned as complex mixtures of bioactive peptides many of which are analogues of endogenous regulatory peptides. While skin secretions can be obtained non-invasively for peptidome analysis, parallel studies on the granular gland transcriptome required specimen sacrifice. The aim of the present study was to analyse archived skin secretions to determine the robustness of bioactive peptide precursor-encoding polyadenylated mRNAs in an attempt to extract maximum molecular information from rare samples. A range of solvated skin secretion samples were examined after lyophilisation for their potential to generate viable and comprehensive cDNA libraries based upon polyadenylated mRNA capture and amplification/cloning using appropriate commercial kits. Here we present unequivocal data that the granular gland transcriptome persists in a PCR amenable format even after storage for as long as 12 years in 0.1%(v/v) aqueous trifluoroacetic acid (TFA). We used a pooled skin secretion sample (2 ml) from the yellow-bellied toad, Bombina variegata (n = 14), containing the equivalent of 5 mg/ml of lyophilised skin secretion, that had been used in part for peptide isolation purposes in 1998 and had been stored at - 20 °C since that time. In the first cloning experiment, 12 different bombinin-like peptide precursor cDNAs were cloned encoding 17 different bombinins, the majority of which were novel. Subsequently, bombesin and bradykinin-related peptide precursor transcripts have been cloned successfully. These data illustrate the unexpected stability/longevity of the transcriptome in these secretions — a finding with implications for both this field of research and for the wider field of molecular biology.

Optimised microwave-assisted synthesis of methylcarbonate salts: a convenient methodology to prepare intermediates for ionic liquid libraries

The reaction of 1-butylpyrrolidine with dimethyl carbonate to yield the ionic liquid precursor, 1-butyl-1-methylpyrrolidinium methylcarbonate, has been investigated under microwave heating conditions and the reaction parameters optimised to achieve 100% yield of the pyrrolidinium salt with no by-products in under 1 h. The reactions of tributylamine, trioctylphosphine, and 1-butylimidazole with dimethyl carbonate under comparable conditions have also been evaluated, yielding the corresponding methylcarbonate salts which can be used as intermediates for the preparation of halide-free ionic liquids without generating any undesirable salt wastes.

Hierarchical VHDL libraries for DSP ASIC design

Methods are presented for the rapid design of DSP ASICs based on the use of hierarchical VHDL libraries. These are portable across many silicon foundries and allow complex DSP silicon systems to be developed in a fraction of the time normally required. Resulting designs are highly competitive with ones created using conventional methods. The approach is illustrated by its application to ADPCM codec and DCT cores.

Rapid design of DSP ASIC cores using hierarchical VHDL libraries

Methods are presented for the rapid design of DSP ASICs based on the use of a series of hierarchical VHDL libraries which are portable across many silicon foundries. These allows complex DSP silicon systems to be developed in a small fraction of the time normally required. Resulting designs are highly competitive with those developed using more conventional methods. The approach is illustrated using several examples. These include ADPCM codecs, as well as DCT and FFT cores.

P2P and SOA architecture for digital libraries

In an information-driven society where the volume and value of produced and consumed data assumes a growing importance, the role of digital libraries gains particular importance. This work analyzes the limitations in current digital library management systems and the opportunities brought by recent distributed computing models. The result of this work is the implementation of the University of Aveiro integrated system for digital libraries and archives. It concludes by analyzing the system in production and proposing a new service oriented digital library architecture supported in a peer-to-peer infrastructure

Marketingstrategies for academic libraries

This assignment is about the development of a general strategic marketing plan for academic libraries in Germany and can be used as a guideline for libraries that want to develop concrete marketing strategies for several products and services. Two examples of marketing projects are at its end presented for linking theoretical approaches to practice. Finally the development of an own marketing strategy for “information literacy” builds the last part of the assignment.

Development of new approaches for the synthesis and decoding of one-bead one-compound cyclic peptide libraries

La plupart des processus cellulaires et biologiques reposent, à un certain niveau, sur des interactions protéine-protéine (IPP). Leur manipulation avec des composés chimiques démontre un grand potentiel pour la découverte de nouveaux médicaments. Malgré la demande toujours croissante en molécules capables d’interrompre sélectivement des IPP, le développement d’inhibiteurs d’IPP est fortement limité par la grande taille de la surface d’interaction. En considérant la nature de cette surface, la capacité à mimer des structures secondaires de protéines est très importante pour lier une protéine et inhiber une IPP. Avec leurs grandes capacités peptidomimétiques et leurs propriétés pharmacologiques intéressan-tes, les peptides cycliques sont des prototypes moléculaires de choix pour découvrir des ligands de protéines et développer de nouveaux inhibiteurs d’IPP. Afin d’exploiter pleinement la grande diversité accessible avec les peptides cycliques, l’approche combinatoire «one-bead-one-compound» (OBOC) est l’approche la plus accessible et puissante. Cependant, l’utilisation des peptides cycliques dans les chimiothèques OBOC est limitée par les difficultés à séquencer les composés actifs après le criblage. Sans amine libre en N-terminal, la dégradation d’Edman et la spectrométrie de masse en tandem (MS/MS) ne peuvent pas être utilisées. À cet égard, nous avons développé de nouvelles approches par ouverture de cycle pour préparer et décoder des chimiothèques OBOC de peptides cycliques. Notre stratégie était d’introduire un résidu sensible dans le macrocycle et comme ancrage pour permettre la linéarisation des peptides et leur largage des billes pour le séquençage par MS/MS. Tout d’abord, des résidus sensibles aux nucléophiles, aux ultraviolets ou au bromure de cyanogène ont été introduits dans un peptide cyclique et leurs rendements de clivage évalués. Ensuite, les résidus les plus prometteurs ont été utilisés dans la conception et le développement d’approches en tandem ouverture de cycle / clivage pour le décodage de chimiothèques OBOC de peptides cycliques. Dans la première approche, une méthionine a été introduite dans le macrocycle comme ancrage pour simultanément permettre l’ouverture du cycle et le clivage des billes par traitement au bromure de cyanogène. Dans la seconde approche, un résidu photosensible a été utilisé dans le macrocycle comme ancrage pour permettre l’ouverture du cycle et le clivage suite à une irradiation aux ultraviolets. Le peptide linéaire généré par ces approches peut alors être efficacement séquencé par MS/MS. Enfin, une chimiothèque OBOC a été préparée et criblée la protéine HIV-1 Nef pour identifier des ligands sélectifs. Le développement de ces méthodologies permttra l’utilisation de composés macrocycliques dans les chimiothèques OBOC et constitue une contribution importante en chimie médicinale pour la découverte de ligands de protéines et le développement d’inhibiteurs d’IPP.

Libraries and Canon-Formation: the Case of English in the Collections of the Library of the Faculty of Humanities, Lisbon University

Abstract: The project for researching the role played by libraries in canon-formation (namely through their policies regarding the creation, organization, preservation, and utilization of the collections) will be presented and discussed. We selected the Library of the Faculty of Humanities, Lisbon University, a modern academic library, created in 1859, by royal decree of D. Pedro V, following his canonical choice. Actually, the two contemporary rulers of new Britannia— Prince Albert, his cousin, and Queen Victoria—held this king in high consideration for his outstanding contribution to Portuguese modernisation. Representing various fields of study, the collections were decisive to canon-formation in the Faculty of Humanities. Thus, we have been trying to answer the following questions: who has been creating, organizing, preserving, and utilizing the collections, from the mid-nineteenth century onwards? When, where and how? Presently, we are studying the collections in English, namely the works belonging or referring to the long nineteenth century. Richard Garnett’s “The International Library of Famous Literature” (London, 1899) is our first case-study. The anthology determined the Western literary, cultural and visual canon at the turning of the century, as evidenced by comparing it to the Portuguese and Spanish editions, published at the beginning of the twentieth century.

Visual Literacy Standards in Higher Education: New Opportunities for Libraries and Student Learning

Visual literacy is essential for 21st century learners. Across the higher education curriculum, students are being asked to use and produce images and visual media in their academic work, and they must be prepared to do so. The Association of College and Research Libraries has published the Visual Literacy Competency Standards for Higher Education, which for the first time, outline specific visual literacy learning outcomes. These Standards present new opportunities for libraries to expand their role in student learning through standards-based teaching and assessment, and to contribute to campus-wide collaborative efforts to develop students’ skills and critical thinking with regard to visual materials.

An algebra and conceptual model for semantic tagging of collaborative digital libraries

Cost-effective semantic description and annotation of shared knowledge resources has always been of great importance for digital libraries and large scale information systems in general. With the emergence of the Social Web and Web 2.0 technologies, a more effective semantic description and annotation, e.g., folksonomies, of digital library contents is envisioned to take place in collaborative and personalised environments. However, there is a lack of foundation and mathematical rigour for coping with contextualised management and retrieval of semantic annotations throughout their evolution as well as diversity in users and user communities. In this paper, we propose an ontological foundation for semantic annotations of digital libraries in terms of flexonomies. The proposed theoretical model relies on a high dimensional space with algebraic operators for contextualised access of semantic tags and annotations. The set of the proposed algebraic operators, however, is an adaptation of the set theoretic operators selection, projection, difference, intersection, union in database theory. To this extent, the proposed model is meant to lay the ontological foundation for a Digital Library 2.0 project in terms of geometric spaces rather than logic (description) based formalisms as a more efficient and scalable solution to the semantic annotation problem in large scale.

Recreational Reading of International Students in Academic Libraries

survey of international students in a university library as to whether or not they engage in recreational reading and if they think it helps their language learning

ESL Collections, University Libraries, and Internationalization

This research study examines the content, types of materials, locations, and library collection development policies concerning ESL (English as a second language) materials collections on university campuses in the United States and Canada. ESL learning materials are defined in this study as those materials supporting adult learners who are non-native speakers of English in a higher education setting. The purpose of this study is to describe the content and types of materials in these collections, to learn where these collections are typically housed on university campuses, to discover what collection development policies may inform the building of these collections, and to explore the potential significance of these collections for university libraries. The overriding question that informs this study is the following: Can involvement with ESL collections serve as a way for university libraries to participate in internationalization by supporting the language needs of international students?

Internationalization in German Academic Libraries: Moving beyond North American Perspectives

This paper explores how internationalization is understood and experienced in German academic libraries. Its main purpose is to move the discussion of internationalization in academic libraries beyond the boundaries of English-speaking North America by investigating a European perspective. Its secondary purpose is to investigate the role of English in German academic libraries. An online survey and a series of in-person interviews conducted in Germany in April 2015 provided the data for this study. What emerged are a series of stated differences and similarities between North America and Germany informed by the two overarching themes of implicit internationalization and plurilingualism, the ability to switch from one language to another as required.