Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

TRICUT: a program to clip triangle meshes using the rapid and triangle libraries and the visualization toolkit

An efficient technique to cut polygonal meshes as a step in the geometric modeling of topographic and geological data has been developed. In boundary represented models of outcropping strata and faulted horizons polygonal meshes often intersect each other. TRICUT determines the line of intersection and re-triangulates the area of contact. Along this line the mesh is split in two or more parts which can be selected for removal. The user interaction takes place in the 3D-model space. The intersection, selection and removal are under graphic control. The visualization of outcropping geological structures in digital terrain models is improved by determining intersections against a slightly shifted terrain model. Thus, the outcrop line becomes a surface which overlaps the terrain in its initial position. The area of this overlapping surface changes with respect to the strike and dip of the structure, the morphology and the offset. Some applications of TRICUT on different real datasets are shown. TRICUT is implemented in C+ + using the Visualization Toolkit in conjunction with the RAPID and TRIANGLE libraries. The program runs under LINUX and UNIX using the MESA OpenGL library. This work gives an example of solving a complex 3D geometric problem by integrating available robust public domain software. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98 % minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65(.)2 %) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10(.)9 %), Spirochaetes (4(.)3 %), Bacteroidetes (6(.)5 %), Actinobacteria (2(.)2 %) and Deferribacteres (2(.)2 %). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

Optimal clone identifier for genomic shotgun libraries: OC Identifier tool

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray. ©FUNPEC-RP.

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.

Report on the Workshop on User Education Techniques for Use in Special Libraries

Informe del Taller efectuado para identificar una definicion de educacion del usuario que sea apropiada para las bibliotecas especializadas del Sistema de Informacion del Caribe; para analizar el punto de vista del usuario de los sistemas de informacion; y para revisar algunas tecnicas que permitan el uso de los medios de comunicacion para llegar al usuario.

Evaluation of indexed language used in collective catalogues of university libraries: a socio-cognitive study using verbal protocol

The use of indexing language in university libraries collective catalogs and the socio-cognitive context of indexing and users were evaluated. The methodology consisted of a diagnostic study elaboration of the functioning and treatment procedures of the indexing information from nine libraries of the UNESP Network, representing the Civil Engineering, Pedagogy and Dentistry areas from a data collection using the Verbal Protocol introspective technique in the Individual and Group forms. The study conducted a reflection upon the statements issued by the seventy-two participating individuals whose the results revealed unsatisfactory results about the use of the Subject Headings List of the BIBLIODATA Network, indexing language utilizing by the UNESP Libraries Network, Brazil, in the representation and in the information retrieval process in the ATHENA catalog, about the sequent aspects of the language: lack of specialized vocabulary as well as updated; lack of remissives and of specific headings, and others. We have concluded that the adequate use of indexing languages of specialized scientific areas becomes by means of evaluation as to updating, specificity and compatibility in order to meet the needs of indexing and information retrieval.

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.

A Survey of Medical College Libraries in Andhra Pradesh, India

Data was collected from 22 selected medical college libraries and 526 undergraduate and postgraduate medical students, using a survey. The article presents a list of findings and recommendations based on them to improve the services of medical college libraries in Andhra Pradesh.

Working Experience and Librarians' Knowledge of Information and Communication Technologies (ICTs) in Nigerian University Libraries

This paper discuses the influence of librarians' years of working experience and sources of acquisition of ICTs' knowledge and skills. The study is based on 169 librarians working in thirteen university libraries in the universities of six states located in the South-South zone of Nigeria. The purpose of the paper is to find out if years of working experience has an effect on librarians' sources/means of acquisition of ICT knowledge and skills. The questionnaires used were answered by two categories of librarians. Those with longer years of experience – 16 years and above and those with fewer years of working experience. It was concluded that librarians with fewer years of working experience explore means of acquiring ICTs knowledge and skills more than librarians with more years of working experience. It was recommended that librarians with longer years of working experience develop more interest in sources through which they can acquire ICT knowledge and skills.