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 integrated lot sizing and cutting stock problem in a furniture factory

This work studies the integrated lot sizing and cutting stock problem, where the goal is to capture the dependency that exists between two important decisions in the production process, in order to economize raw materials and also reduce production and inventory costs. The integrated lot sizing and cutting stock problem is studied in a small furniture factory that produces wardrobes, dressing tables and cupboards and the lot sizing and cutting stock decisions are taken by the production manager. A column-generation technique is used to solve a linear relaxation of the proposed model. The computational results, using real data from the factory, show that it is possible to reduce total inventory and raw material costs when integrated planning is used. © 2013 IFAC.

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.

FROM FACTORY-FLOOR TO UNIVERSITY

The interaction between industry and university is often discussed. Industry participants feel they do not have enough time to spend with academics because of tight deadlines to achieve your goals. The other hand, professors and his students do not have availability and resources for responding quickly to industry activities. Both sides recognize the associated problems and feel the consequences of various forms. One way to reduce the distance between them is to provide industrial labs that resemble the factory floor at the university. Thus not only students may work on a real technological base, but also the industry's problems can be brought to the university laboratory. To ensure that relevant industrial problems will be studied, the industry needs help in the formulation of the problem being researched. The graduate program of Automation and Control Engineering from UNESP Sorocaba is aimed at training human resources with skills in automation and control activities related to the development of automatic control processes, integrating electronic commands, intelligent manufacturing and industrial robotics. In order to achieve its objectives, one of the pillars of the university consists of a wide range of modern equipments and software for industrial automation, which allows the circuit assembly from most primitive until configuration and programming of a complex system of integrated manufacturing. This paper describes industrial automation equipments and laboratory structure offered to students of Control and Automation Engineering graduate program at UNESP Sorocaba as alternative to close technologies and real problems on the job until academic world. The strategic is to do students understand theory and operations in robotic and industrial automation by means to manipulating real production systems locate at university