Display of a Maize cDNA library on baculovirus infected insect cells

Background: Maize is a good model system for cereal crop genetics and development because of its rich genetic heritage and well-characterized morphology. The sequencing of its genome is well advanced, and new technologies for efficient proteomic analysis are needed. Baculovirus expression systems have been used for the last twenty years to express in insect cells a wide variety of eukaryotic proteins that require complex folding or extensive posttranslational modification. More recently, baculovirus display technologies based on the expression of foreign sequences on the surface of Autographa californica ( AcMNPV) have been developed. We investigated the potential of a display methodology for a cDNA library of maize young seedlings. Results: We constructed a full-length cDNA library of young maize etiolated seedlings in the transfer vector pAcTMVSVG. The library contained a total of 2.5 x 10(5) independent clones. Expression of two known maize proteins, calreticulin and auxin binding protein (ABPI), was shown by western blot analysis of protein extracts from insect cells infected with the cDNA library. Display of the two proteins in infected insect cells was shown by selective biopanning using magnetic cell sorting and demonstrated proof of concept that the baculovirus maize cDNA display library could be used to identify and isolate proteins. Conclusion: The maize cDNA library constructed in this study relies on the novel technology of baculovirus display and is unique in currently published cDNA libraries. Produced to demonstrate proof of principle, it opens the way for the development of a eukaryotic in vivo display tool which would be ideally suited for rapid screening of the maize proteome for binding partners, such as proteins involved in hormone regulation or defence.

Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli

Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Coconut, Cocos nucifera L. is a major plantation crop, which ensures income for millions of people in the tropical region. Detailed molecular studies on zygotic embryo development would provide valuable clues for the identification of molecular markers to improve somatic embryogenesis. Since there is no ongoing genome project for this species, coconut expressed sequence tags (EST) would be an interesting technique to identify important coconut embryo specific genes as well as other functional genes in different biochemical pathways. The goal of this study was to analyse the ESTs by examining the transcriptome data of the different embryo tissue types together with one somatic tissue. Here, four cDNA libraries from immature embryo, mature embryo, microspore derived embryo and mature leaves were constructed. cDNA was sequenced by the Roche-454 GS-FLX system and assembled into 32621 putative unigenes and 155017 singletons. Of these unigenes, 18651 had significant sequence similarities to non-redundant protein database, from which 16153 were assigned to one or more gene ontology categories. Homologue genes, which are responsible for embryo development such as chitinase, beta-1,3-glucanase, ATP synthase CF0 subunit, thaumatin-like protein and metallothionein-like protein were identified among the embryo EST collection. Of the unigenes, 6694 were mapped into 139 KEGG pathways including carbohydrate metabolism, energy metabolism, lipid metabolism, amino acid metabolism and nucleotide metabolism. This collection of 454-derived EST data generated from different tissue types provides a significant resource for genome wide studies and gene discovery of coconut, a non-model species.

Digitisation, representation, and formalisation - Digital libraries of mathematics

One of the main tasks of the mathematical knowledge management community must surely be to enhance access to mathematics on digital systems. In this paper we present a spectrum of approaches to solving the various problems inherent in this task, arguing that a variety of approaches is both necessary and useful. The main ideas presented are about the differences between digitised mathematics, digitally represented mathematics and formalised mathematics. Each has its part to play in managing mathematical information in a connected world. Digitised material is that which is embodied in a computer file, accessible and displayable locally or globally. Represented material is digital material in which there is some structure (usually syntactic in nature) which maps to the mathematics contained in the digitised information. Formalised material is that in which both the syntax and semantics of the represented material, is automatically accessible. Given the range of mathematical information to which access is desired, and the limited resources available for managing that information, we must ensure that these resources are applied to digitise, form representations of or formalise, existing and new mathematical information in such a way as to extract the most benefit from the least expenditure of resources. We also analyse some of the various social and legal issues which surround the practical tasks.

Libraries and literature in Rome

A chapter of 6,000 words on books, literary culture, and public and private libraries in the ancient city of Rome

Public libraries in the cities of the Roman Empire

A chapter based on a paper given at major conference, arguing that the civic and architectural contexts of many public libraries in the Roman world contributed strongly to their status as conspicuous 'public' buildings, and should inform the way we think of library functions in the Roman world

Galen and libraries in the Peri Alupias

A long (12,000 word) article on the evidence for library function and usage in the newly-discovered Peri Alupias of Galen

Bibliotheca Latina Graecaque: on the possible division of Roman libraries by language

An article challenging the frequent assumption that Roman public libraries consisted of architecturally separated spaces divided by language (Latin and Greek). While the evidence for such a division is reasonably strong in some cases, in others it is convention rather than evidence that prompts the labelling of buildings as 'Latin' and 'Greek' libraries. The article is based on a paper given at a major international conference in Paris

Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price

The mechanism of action and properties of a solid-phase ligand library made of hexapeptides (combinatorial peptide ligand libraries or CPLL), for capturing the "hidden proteome", i.e. the low- and very low-abundance proteins constituting the vast majority of species in any proteome, as applied to plant tissues, are reviewed here. Plant tissues are notoriously recalcitrant to protein extraction and to proteome analysis. Firstly, rigid plant cell walls need to be mechanically disrupted to release the cell content and, in addition to their poor protein yield, plant tissues are rich in proteases and oxidative enzymes, contain phenolic compounds, starches, oils, pigments and secondary metabolites that massively contaminate protein extracts. In addition, complex matrices of polysaccharides, including large amount of anionic pectins, are present. All these species compete with the binding of proteins to the CPLL beads, impeding proper capture and identification / detection of low-abundance species. When properly pre-treated, plant tissue extracts are amenable to capture by the CPLL beads revealing thus many new species among them low-abundance proteins. Examples are given on the treatment of leaf proteins, of corn seed extracts and of exudate proteins (latex from Hevea brasiliensis). In all cases, the detection of unique gene products via CPLL capture is at least twice that of control, untreated sample.

Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price

The mechanism of action and properties of a solid-phase ligand library made of hexapeptides (combinatorial peptide ligand libraries or CPLL, for capturing the "hidden proteome", i.e. the low- and very low-abundance proteins Constituting the vast majority of species in any proteome. as applied to plant tissues, are reviewed here. Plant tissues are notoriously recalcitrant to protein extraction and to proteome analysis, Firstly, rigid plant cell walls need to be mechanically disrupted to release the cell content and, in addition to their poor protein yield, plant tissues are rich in proteases and oxidative enzymes, contain phenolic Compounds, starches, oils, pigments and secondary metabolites that massively contaminate protein extracts. In addition, complex matrices of polysaccharides, including large amount of anionic pectins, are present. All these species compete with the binding of proteins to the CPLL beads, impeding proper capture and identification I detection of low-abundance species. When properly pre-treated, plant tissue extracts are amenable to capture by the CPLL beads revealing thus many new species among them low-abundance proteins. Examples are given on the treatment of leaf proteins, of corn seed extracts and of exudate proteins (latex from Hevea brasiliensis). In all cases, the detection of unique gene products via CPLL Capture is at least twice that of control, untreated sample. (c) 2008 Elsevier B.V. All rights reserved.

Amphioxus type I keratin cDNA and the evolution of intermediate filament genes

We report the cloning of an intermediate filament (IF) cDNA from the cephalochordate amphioxus that encodes a protein assignable to the type I keratin group. This is the first type I keratin reported from an invertebrate. Molecular phylogenetic analyses reveal that amphioxus also possesses a type II keratin, and that the genes encoding short-rod IF proteins underwent different patterns of duplication in vertebrates and their closest relatives, the cephalochordates. Extensive IF gene duplication and divergence may have facilitated the origin of new specialised cell types in vertebrates.

Roman public libraries

This thesis aims to investigate the development and functions of public libraries in Rome and the Roman world. After a preface with maps of libraries in Rome, Section I discusses the precursors for public library provision in the private book collections of Republican Rome, and their transfer into the public domain with the first public libraries of Asinius Pollio and Augustus. Section II contains three 'case studies' of public libraries' different roles. The Augustan library programme is used in Ch.II.l to examine the role of imperial public libraries in literary life and the connections between Rome's libraries and those of Alexandria. Chapter II.2 concentrates on the libraries of Trajan's Forum to explore the intersection of imperial public libraries and monumental public architecture. This chapter responds to an important recent article by arguing for the continued identification of the Forum's libraries with twin brick buildings at its northern end, and suggests a series of correspondences between these libraries and its other monumental components. The conclusions of this chapter are important when considering the public libraries of the wider empire, several of which seem to have been inspired by the Trajanic libraries. Chapter II.3 considers imperial public libraries and leisure by looking at the evidence for libraries within bath-house complexes, concluding that their presence there is consistent with the archaeological and epigraphic evidence and fits in well with what we know of the intellectual and cultural life of these structures. Section III examines various aspects of the practical function of Roman public libraries: their contents (books and archives), division into Latin and Greek sections, provisions for shelving and cataloguing, staff, usership, architectural form, decoration, and housing of works of art. The picture that emerges is of carefully designed and functional buildings intended to sustain public, monumental, and practical functions. Section IV uses a variety of texts to examine the way in which libraries were viewed and used. Ch. IV. 1 discusses the evidence for use of libraries by scholars and authors such as Gellius, Galen, Josephus, and Apuleius. Ch. IV.2 examines parallels between library collections and compendious encyclopaedic elements within Roman literature and considers how library collections came to be canon-forming institutions and vehicles for the expression of imperial approval or disapproval towards authors. The channels through which this imperial influence flowed are investigated in Ch. IV.3, which looks at the directors and staff of the public libraries of Rome. The final section (V) of the thesis concerns public libraries outside the city of Rome. Provincial libraries provide a useful case study in 'Romanisation': they reveal a range of influences and are shown to embody local, personal, and metropolitan imperial identities. There follows a brief conclusion, and a bibliography. There are also five appendices of numismatic and epigraphic material discussed in the text. This material has not been adequately or completely gathered elsewhere and is intended to assist the reader; where appropriate it includes illustrations, transcriptions, and translations.

An investigation into the viability of LibraryThing for promotional and user engagement purposes in libraries

Structured abstract: Purpose: LibraryThing is a Web 2.0 tool allowing users to catalogue books using data drawn from sources such as Amazon and the Library of Congress and has facilities such as tagging and interest groups. This study evaluates whether LibraryThing is a valuable tool for libraries to use for promotional and user engagement purposes. Methodology: This study used a sequential mixed methods 3 phase design: (1) the identification of LibraryThing features for user engagement or promotional purposes, (2) exploratory semi-structured interviews (3) a questionnaire. Findings: Several uses of LibraryThing for promotional and user engagement purposes were identified. The most popular reason libraries used LibraryThing was to promote the library or library stock, with most respondents using it specifically to highlight collections of books. Monitoring of patron usage was low and many respondents had not received any feedback. LibraryThing was commonly reported as being easy to use, remotely accessible, and having low cost, whilst its main drawbacks were the 200 book limit for free accounts, and it being a third-party site. The majority of respondents felt LibraryThing was a useful tool for libraries. Practical implications: LibraryThing has most value as a promotional tool for libraries. Libraries should actively monitor patron usage of their LibraryThing account or request user feedback to ensure that LibraryThing provides a truly valuable service for their library. Orginality : There is little research on the value of LibraryThing for libraries, or librarians perceptions of LibraryThing as a Web 2.0 tool.