Routine libraries for pattern recognition in quasispecies.

The results obtained through biological research usually need to be analyzed using computational tools, since manual analysis becomes unfeasible due to the complexity and size of these results. For instance, the study of quasispecies frequently demands the analysis of several, very lengthy sequences of nucleotides and amino acids. Therefore, bioinformatics tools for the study of quasispecies are constantly being developed due to different problems found by biologists. In the present study, we address the development of a software tool for the evaluation of population diversity in quasispecies. Special attention is paid to the localization of genome regions prone to changes, as well as of possible hot spots.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

The University and its libraries: Reactions and resistance to scientific publishers

This paper addresses the relationship of copyright and the right of universities on scientific production. Information and Communication Technologies (ICTs) are causing many changes in the system of scientific communication, such as the creation of Institutional Repositories that aim to gather scientific production in digital format. The University needs quicker ways of spreading academic production and many questions are emerging due to contexts such as the Open Access movement. Thus, this paper questions the positioning of Universities, especially Public Universities, which despite having policies related to intellectual property to protect the transferring forms of research results to society; many times do not have a positioning or a mechanism that regulates the self-deposit of scientific production in these Institutional Repositories. In order to develop this paper, the following issues are addressed: lack of interest of the University in storing scientific production; reports on the relationship of the library with scientific publishing houses; the participation of faculty members and students in supporting the Free Access movement; and initiatives aimed at greater flexibility of copyright to the context of scientific production. In order to follow the development of these issues at international level, it was opted for qualitative research with non-participating direct observation to carry out the identification and description of copyright policy of important publishers from the ROMEO SHERPA site; therefore, it can be observed that there are changes regarding the publishers' flexibility before self-archiving of authors in open access institutional repositories in their universities. Given this scenario, we presente reflections and considerations that involve the progress and mainly the integration of the University and its faculty members; the institution should recommend and guide its faculty members not to transfer their copyrights, but to defend their right of copy to Institutional Repositories along with Publishing Houses.

Screening of genomic libraries

Microsatellites, or simple sequence repeats (SSRs), have proven to be an important molecular marker in plant genetics and breeding research. The main strategies to obtain these markers can be through genomic DNA and from expressed sequence tags (ESTs) from mRNA/cDNA libraries. Genetic studies using microsatellite markers have increased rapidly because they can be highly polymorphic, codominant markers and they show heterozygous conserved sequences. Here, we describe a methodology to obtain microsatellite using the enrichment library of DNA genomic sequences. This method is highly efficient to development microsatellite markers especially in plants that do not have available ESTs or genome databases. This methodology has been used to enrich SSR marker libraries in Citrus spp., an important tool to genotype germplasm, to select zygotic hybrids, and to saturate genetic maps in breeding programs. © Springer Science+Business Media, LLC 2013.

The University and its libraries: reactions and resistance to scientific publishers

This paper addresses the relationship of copyright and the right of universities on scientific production. Information and Communication Technologies (ICTs) are causing many changes in the system of scientific communication, such as the creation of Institutional Repositories that aim to gather scientific production in digital format. The University needs quicker ways of spreading academic production and many questions are emerging due to contexts such as the Open Access movement. Thus, this paper questions the positioning of Universities, especially Public Universities, which despite having policies related to intellectual property to protect the transferring forms of research results to society; many times do not have a positioning or a mechanism that regulates the self-deposit of scientific production in these Institutional Repositories. In order to develop this paper, the following issues are addressed: lack of interest of the University in storing scientific production; reports on the relationship of the library with scientific publishing houses; the participation of faculty members and students in supporting the Free Access movement; and initiatives aimed at greater flexibility of copyright to the context of scientific production. In order to follow the development of these issues at international level, it was opted for qualitative research with non-participating direct observation to carry out the identification and description of copyright policy of important publishers from the ROMEO SHERPA site; therefore, it can be observed that there are changes regarding the publishers' flexibility before self-archiving of authors in open access institutional repositories in their universities. Given this scenario, we presente reflections and considerations that involve the progress and mainly the integration of the University and its faculty members; the institution should recommend and guide its faculty members not to transfer their copyrights, but to defend their right of copy to Institutional Repositories along with Publishing Houses.

Theses, Projects, and Africana Materials Management in Nigerian Academic Libraries: The Case of Hezekiah Oluwasanmi Library

This is a survey of the procurement, organization and use of unpublished projects, theses, and Africana mateials in Hezekiah Oluwasanmi Library, Obafemi Awolowo University, Ile-Ife, Nigeria. The Africana section conserves knowledge, preserves cultural heritage, provides information, and supports education and research. This paper the location, mode of processing, circulation, and terms of availability of these materials. Recommendations are made on how to manage Africana materials in academic libraries where they constitute a vital component of collections.

DIGITAL LIBRARIES AND LEARNING OBJECTS REPOSITORIES

Discusses the technological changes that affects learning organizations as well as the human, technical, legal and sustainable aspects regarding learning objects repositories creation, maintenance and use. It presents concepts of information objects and learning objects, the functional requirements needed to their storage at Learning Management Systems. The role of Metadata is reviewed concerning learning objects creation and retrieval, followed by considerations about learning object repositories models, community participation/collaborative strategies and potential derived metrics/indicators. As a result of this desktop research, it can be said that not only technical competencies are critical to any learning objects repository implementation, but it urges that an engaged community of interest be establish as a key to support a learning object repository project. On that matter, researchers are applying Activity Theory (Vygostky, Luria y Leontiev) in order to seek joint perceptions and actions involving learning objects repository users, curators and managers, perceived as critical assets to a successful proposal.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Abstract Background From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas.

Quality evaluation of tandem mass spectral libraries

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

MARVIN: a medical research application framework based on open source software

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Aiming at improving access to research output through the institutional repository

The paper is to introduce the institutional repository (IR) as a powerful tool to support the researchers of the institution to archive and disseminate their research findings freely to the scholarly community on the Internet. The IR can improve the access to an institution’s research output enormously. The operations of an IR also require various interactions with researchers, which enables the library to gain a solid understanding of research needs and expectations. Through such interaction, the relationship and mutual trust between researchers and the library are strengthened. The experiences of the Institute of Developing Economies (IDE) library can be useful to other special libraries.

Integration of Virtual Map Rooms as a support tool in historical and social research

At the present time almost all map libraries on the Internet are image collections generated by the digitization of early maps. This type of graphics files provides researchers with the possibility of accessing and visualizing historical cartographic information keeping in mind that this information has a degree of quality that depends upon elements such as the accuracy of the digitization process and proprietary constraints (e.g. visualization, resolution downloading options, copyright, use constraints). In most cases, access to these map libraries is useful only as a first approach and it is not possible to use those maps for scientific work due to the sparse tools available to measure, match, analyze and/or combine those resources with different kinds of cartography. This paper presents a method to enrich virtual map rooms and provide historians and other professional with a tool that let them to make the most of libraries in the digital era.

Research Objects

In the domain of eScience, investigations are increasingly collaborative. Most scientific and engineering domains benefit from building on top of the outputs of other research: By sharing information to reason over and data to incorporate in the modelling task at hand. This raises the need to provide means for preserving and sharing entire eScience workflows and processes for later reuse. It is required to define which information is to be collected, create means to preserve it and approaches to enable and validate the re-execution of a preserved process. This includes and goes beyond preserving the data used in the experiments, as the process underlying its creation and use is essential. This tutorial thus provides an introduction to the problem domain and discusses solutions for the curation of eScience processes.