Diseño y realización de una base de datos para el control de inventario del Museo Historia de la Informática

El objetivo principal de este proyecto es la realización de un sistema, que permita a través de alguna herramienta accesible a cualquier usuario, poder interactuar con una base de datos que contenga un catálogo bien documentado de los objetos disponibles en el Museo Histórico de la Informática (MHI) perteneciente a la Escuela Técnica Superior de Ingenieros Informáticos (ETSIINF) de la Universidad Politécnica de Madrid (UPM). Hasta el momento, no existía inventario alguno, por lo que la contribución del trabajo que aquí se presenta, supone un gran avance en la organización de los fondos del Museo. Ello contribuirá al desarrollo del objetivo principal del MHI, que es la difusión de la historia de la informática, mediante un medio de los más usados hoy en día, internet. El trabajo realizado se presenta a lo largo de 10 capítulos. En los que se muestran, el análisis del problema, los requisitos y las distintas alternativas posibles de solución, así como la solución adoptada y su desarrollo, tanto en el diseño de la base de datos como de sitio Web que hace posible la visualización e interacción de la información. En el primer capítulo, se puede encontrar una breve introducción del proyecto. Se indican los objetivos, la motivación y el alcance del mismo. En el segundo capítulo, se muestran los requisitos del problema, se analizan las tecnologías, herramientas y lenguajes disponibles para diseñar bases de datos, y se propone la elección de una de las tecnologías, teniendo en cuenta las limitaciones del entorno en el cual se va a implantar la solución. En el tercer capítulo, se diseña la solución propuesta para el sistema. Primero se muestra el diseño de bajo nivel, que serán los cimientos y posteriormente se explica el diseño de alto nivel. Finalmente, se introduce el conjunto de pruebas que el sistema tendrá que pasar para garantizar su correcto funcionamiento. El cuarto capítulo, muestra todas las tecnologías, herramientas, lenguajes y plantillas utilizadas para la implementación de la WEB. Mientras que en el capítulo cinco, se pueden ver los resultados de las pruebas realizadas. En el capítulo seis, se evalúan los costes económicos de realización de proyecto y se presenta la agenda de actividades y tareas llevadas a cabo para su desarrollo. El séptimo capítulo, resume las contribuciones técnicas del proyecto tratadas en los capítulos anteriores, así como las conclusiones personales. Mientras que, el capítulo ocho, apunta una serie de trabajos futuros que se podrían realizarse utilizando como base este proyecto. El capítulo nueve contiene las referencias de la información que se han consultado y que se citan en el texto, y el décimo complementa este proceso de información, incluyendo un glosario de términos técnicos. El contenido de la memoria concluye con el manual de usuario para la administración de la base de datos, que se incluye en forma de anexo.---ABSTRACT---The main goal of this project is the development of a system that would allow through some accessible tool for any user to interact with a database that contains a well-documented objects available in the Computer History Museum's (MHI) catalog, which belongs to the School of Computer Engineers (ETSIINF) of the Polytechnic University of Madrid (UPM). So far, there was no inventory, so the contribution of the work presented here, is a breakthrough in the organization of the Museum's collections. This will contribute to the development of the main goal of the MHI, which is the diffusion of computer history, by means of the most used today, internet. The work is presented along 10 chapters. Which show the analysis of the problem, requirements, the different possible solutions and the solution adopted and its development, both in the design of the database and Web site, which enables the visualization and interaction of the information. In the first chapter, a brief introduction of the project is found. Objectives, motivation and scope of the project are specified. In the second chapter, the requirements of the problem are shown. Technologies, tools and languages available to design databases are analysed, and the choice of a technology is proposed, taking into account the limitations of the environment in which it will to implement the solution. In the third chapter, the proposed system solution is designed. First, low-level design, which will be the foundation of the project, is shown, and then the high-level design is explained. Finally, test suite, which the system will have to past to ensure their proper functioning, are introduced. The fourth chapter shows all technologies, tools, languages and templates used to implement the WEB. While in chapter five, the results of the tests are shown. The economic costs of development the project are evaluated in chapter six, and the schedule of activities and tasks carried out for this development are shown. The seventh chapter summarizes the technical contributions of the project discussed in previous chapters, as well as personal conclusions. While the eighth chapter, suggests future works that could be made, based on this project. Ninth chapter contains references to information that have been consulted and cited in the text, and the tenth chapter includes a glossary of technical terms, to complement that process of information. Finally an annex includes a user manual for managing the database.

Multifunctional core–shell Co–SiO2 nanowires via electrodeposition and sol–gel techniques

In this work, we propose a new strategy for the synthesis of multifunctional nanowires using a combination of sol–gel and electrodeposition techniques, based on a two-step procedure. First of all, nanotubes of SiO2 are synthesized via a sol–gel technique using polycarbonate membranes as templates. Homogenous nanotubes are obtained after centrifugation and thermal annealing. Afterwards, a ferromagnetic cobalt core is grown using potentiostatic electrodeposition. Finally, the core–shell Co–SiO2 nanowires are released by dissolving the template using wet-etching. These nanodevices can be used for many detection and sensing purposes. As a proof of concept, we have developed a pH nanosensor by including a pH-sensitive organic dye in the SiO2 shell. The sensing principle is based on the optical response of the organic dye towards pH when added to a solution. The magnetic core allows the recovery of the nanosensors after use. These nanowires can therefore be used as recoverable pH nanosensors. By changing the dye molecule to another molecule or receptor, the procedure described in the paper can be used to synthesize nanodevices for many different applications.

ESTUDO DAS FORMAS E DIMENSÕES LINGUAIS DAS ARCADAS DENTÁRIAS EM INDIVÍDUOS BRASILEIROS COM OCLUSÃO NORMAL

A preocupação com o estudo das formas e dimensões das arcadas dentárias sempre esteve presente na ciência ortodôntica. Para a Ortodontia Lingual, que surgiu no final da década de 70, o primeiro artigo publicado foi o Fujita, onde relatou sobre a forma do arco a ser utilizado nesta técnica, a forma de cogumelo. Apesar de estar sendo divulgada de uma maneira mais intensa nestes últimos anos como uma solução estética definitiva e eficaz, o enfoque dos estudos sobre esta técnica tem sido a fabricação de novos materiais, técnicas de montagem do aparelho lingual e soluções clínicas, com poucas menções sobre a morfologia das arcadas dentárias. O presente trabalho tem a finalidade de estudar as formas e dimensões linguais das arcadas dentárias de indivíduos leucodermas com oclusão normal. Foram utilizados 47 pares de modelos de gesso de oclusão normal digitalizados pela face olcusal, previamente desgastadas até o terço médio da coroa para proporcionar melhor visualização. Por meio do programa CorelDraw 12 foram determinados pontos de referências e criados alguns pontos virtuais necessários para a realização das medidas. Os resultados determinaram três formas das arcadas dentárias linguais: cogumelo, árvore de Natal e mista. A maior prevalência foi a forma árvore de Natal, mas quando analisadas separadamente as arcadas dentárias linguais, encontrados no superior, maior prevalência da forma de cogumelo e no inferior da forma árvore de Natal. Conseqüentemente, esta foi a combinação mais prevalente entre as arcadas dentárias linguais superiores e inferiores. Propusemos diagramas para conformação de arcos ortodônticos linguais com base nos valores obtidos da amostra, determinando-se o quartil 1, mediana e quartil 3, como definidores dos tamanhos pequeno, médio e grande.

ESTUDO DAS FORMAS E DIMENSÕES LINGUAIS DAS ARCADAS DENTÁRIAS EM INDIVÍDUOS BRASILEIROS COM OCLUSÃO NORMAL

A preocupação com o estudo das formas e dimensões das arcadas dentárias sempre esteve presente na ciência ortodôntica. Para a Ortodontia Lingual, que surgiu no final da década de 70, o primeiro artigo publicado foi o Fujita, onde relatou sobre a forma do arco a ser utilizado nesta técnica, a forma de cogumelo. Apesar de estar sendo divulgada de uma maneira mais intensa nestes últimos anos como uma solução estética definitiva e eficaz, o enfoque dos estudos sobre esta técnica tem sido a fabricação de novos materiais, técnicas de montagem do aparelho lingual e soluções clínicas, com poucas menções sobre a morfologia das arcadas dentárias. O presente trabalho tem a finalidade de estudar as formas e dimensões linguais das arcadas dentárias de indivíduos leucodermas com oclusão normal. Foram utilizados 47 pares de modelos de gesso de oclusão normal digitalizados pela face olcusal, previamente desgastadas até o terço médio da coroa para proporcionar melhor visualização. Por meio do programa CorelDraw 12 foram determinados pontos de referências e criados alguns pontos virtuais necessários para a realização das medidas. Os resultados determinaram três formas das arcadas dentárias linguais: cogumelo, árvore de Natal e mista. A maior prevalência foi a forma árvore de Natal, mas quando analisadas separadamente as arcadas dentárias linguais, encontrados no superior, maior prevalência da forma de cogumelo e no inferior da forma árvore de Natal. Conseqüentemente, esta foi a combinação mais prevalente entre as arcadas dentárias linguais superiores e inferiores. Propusemos diagramas para conformação de arcos ortodônticos linguais com base nos valores obtidos da amostra, determinando-se o quartil 1, mediana e quartil 3, como definidores dos tamanhos pequeno, médio e grande.

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

A universal base that is capable of substituting for any of the four natural bases in DNA would be of great utility in both mutagenesis and recombinant DNA experiments. This paper describes the properties of oligonucleotides incorporating two degenerate bases, the pyrimidine base 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one and the purine base N6-methoxy-2,6-diaminopurine, designated P and K, respectively. An equimolar mixture of the analogues P and K (called M) acts, in primers, as a universal base. The thermal stability of oligonucleotide duplexes were only slightly reduced when natural bases were replaced by P or K. Templates containing the modified bases were copied by Taq polymerase; P behaved as thymine in 60% of copying events and as cytosine in 40%, whereas K behaved as if it were guanine (13%) or adenine (87%). The dUTPase gene of Caenorhabditis elegans, which we have found to contain three nonidentical homologous repeats, was used as a model system to test the use of these bases in primers for DNA synthesis. A pair of oligodeoxyribonucleotides, each 20 residues long and containing an equimolar mixture of P and K at six positions, primed with high specificity both T7 DNA polymerase in sequencing reactions and Taq polymerase in PCRs; no nonspecific amplification was obtained on genomic DNA of C. elegans. Use of P and K can significantly reduce the complexity of degenerate oligonucleotide mixtures, and when used together, P and K can act as a universal base.

Targeting a SWI/SNF-related chromatin remodeling complex to the β-globin promoter in erythroid cells

Chromatin remodeling complexes such as the SWI/SNF complex make DNA accessible to transcription factors by disrupting nucleosomes. However, it is not known how such complexes are targeted to the promoter. For example, a SWI/SNF1-like chromatin remodeling complex erythroid Krüppel-like factor (EKLF) coactivator-remodeling complex 1 (E-RC1) disrupts the nucleosomes over the human β-globin promoter in an EKLF-dependent manner. However, it is not known whether E-RC1 is targeted specifically to the β-globin promoter or whether E-RC1 is randomly targeted, but its activity is evident only at the β-globin promoter. Because E-RC1 cannot remodel chromatin over the β-globin promoter without EKLF in vitro, it has been proposed that SWI/SNF1-like complexes such as E-RC1 are targeted specifically to the promoter by selectively interacting with promoter-associated transcription factors such as EKLF. In this report, we test this hypothesis in the cellular context by using the ProteIN POsition Identification with Nuclease Tail (PIN*POINT) assay. We find that the Brahma-related gene (BRG) 1 and BRG1-associated factor (BAF) 170 subunits of E-RC1 are both recruited near the transcription initiation site of the β-globin promoter. On transiently transfected templates, both the locus control region and the EKLF-binding site are important for their recruitment to the β-globin promoter in mouse erythroleukemia cells. When the β-globin promoter was linked to the cytomegalovirus enhancer, the E-RC1 complex was not recruited, suggesting that recruitment of the E-RC1 complex is not a general property of enhancers.

Identification and classification of 16 new kinesin superfamily (KIF) proteins in mouse genome

KIF (kinesin superfamily) proteins are microtubule-dependent molecular motors that play important roles in intracellular transport and cell division. The extent to which KIFs are involved in various transporting phenomena, as well as their regulation mechanism, are unknown. The identification of 16 new KIFs in this report doubles the existing number of KIFs known in the mouse. Conserved nucleotide sequences in the motor domain were amplified by PCR using cDNAs of mouse nervous tissue, kidney, and small intestine as templates. The new KIFs were studied with respect to their expression patterns in different tissues, chromosomal location, and molecular evolution. Our results suggest that (i) there is no apparent tendency among related subclasses of KIFs of cosegregation in chromosomal mapping, and (ii) according to their tissue distribution patterns, KIFs can be divided into two classes–i.e., ubiquitous and specific tissue-dominant. Further characterization of KIFs may elucidate unknown fundamental phenomena underlying intracellular transport. Finally, we propose a straightforward nomenclature system for the members of the mouse kinesin superfamily.

Altered 3′-terminal RNA structure in phage Qβ adapted to host factor-less Escherichia coli

The RNA phage Qβ requires for the replication of its genome an RNA binding protein called Qβ host factor or Hfq protein. Our previous results suggested that this protein mediates the access of replicase to the 3′-end of the Qβ plus strand RNA. Here we report the results of an evolutionary experiment in which phage Qβ was adapted to an Escherichia coli Q13 host strain with an inactivated host factor (hfq) gene. This strain initially produced phage at a titer ≈10,000-fold lower than the wild-type strain and with minute plaque morphology, but after 12 growth cycles, phage titer and plaque size had evolved to levels near those of the wild-type host. RNAs isolated from adapted Qβ mutants were efficient templates for replicase without host factor in vitro. Electron microscopy showed that mutant RNAs, in contrast to wild-type RNA, efficiently interacted with replicase at the 3′-end in the absence of host factor. The same set of four mutations in the 3′-terminal third of the genome was found in several independently evolved phage clones. One mutation disrupts the base pairing of the 3′-terminal CCCoh sequence, suggesting that the host factor stimulates activity of the wild-type RNA template by melting out its 3′-end.

Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase

RNA templates of 33 nucleotides containing the brome mosaic virus (BMV) core subgenomic promoter were used to determine the promoter elements recognized by the BMV RNA-dependent RNA polymerase (RdRp) to initiate RNA synthesis. Nucleotides at positions −17, −14, −13, and −11 relative to the subgenomic initiation site must be maintained for interaction with the RdRp. Changes to every other nucleotide at these four positions allow predictions for the base-specific functional groups required for RdRp recognition. RdRp contact of the nucleotide at position −17 was suggested with a template competition assay. Comparison of the BMV subgenomic promoter to those from other plant and animal alphaviruses shows a remarkable degree of conservation of the nucleotides required for BMV subgenomic RNA synthesis. We show that the RdRp of the plant-infecting BMV is capable of accurately, albeit inefficiently, initiating RNA synthesis from the subgenomic promoter of the animal-infecting Semliki Forest virus. The sequence-specific recognition of RNA by the BMV RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.

Binding of RNA template to a complex of HIV-1 reverse transcriptase/primer/template

HIV-1 reverse transcriptase (RT) catalyzes the synthesis of DNA from DNA or RNA templates. During this process, it must transfer its primer from one template to another RNA or DNA template. Binary complexes made of RT and a primer/template bind an additional single-stranded RNA molecule of the same nucleotide sequence as that of the DNA or RNA template. The additional RNA strand leads to a 10-fold decrease of the off-rate constant, koff, of RT from a primer/DNA template. In a binary complex of RT and a primer/template, the primer can be cross-linked to both the p66 and p51 subunits. Depending on the location of the photoreactive group in the primer, the distribution of the cross-linked primers between subunits is dependent on the nature of the template and of the additional single-stranded molecule. Greater cross-linking of the primer to p51 occurs with DNA templates, whereas cross-linking to p66 predominates with RNA templates. Excess single-stranded DNA shifts the distribution of cross-linking from p66 to p51 with RNA templates, and excess single-stranded RNA shifts the cross-linking from p51 to p66 with DNA templates. RT thus uses two primer/template binding modes depending on the nature of the template.

Purified histone acetyltransferase complexes stimulate HIV-1 transcription from preassembled nucleosomal arrays

Protein acetylation has been implicated in the regulation of HIV-1 gene transcription. Here, we have exploited the activities of four native histone acetyltransferase (HAT) complexes from yeast to directly test whether acetylation regulates HIV-1 transcription in vitro. HAT activities acetylating either histone H3 (SAGA, Ada, and NuA3) or H4 (NuA4) stimulate HIV-1 transcription from preassembled nucleosomal templates in an acetyl CoA-dependent manner. HIV-1 transcription from histone-free DNA is not affected by the HATs, indicating that these activities function in a chromatin-specific fashion. For Ada and NuA4, we demonstrate that acetylation of only histone proteins mediates enhanced transcription, suggesting that these complexes facilitate transcription at least in part by modifying histones. To address a potential mechanism by which HAT complexes stimulate transcription, we performed a restriction enzyme accessibility analysis. Each of the HATs increases the cutting efficiencies of restriction endonucleases targeting the HIV-1 chromatin templates in a manner not requiring transcription, suggesting that histone acetylation leads to nucleosome remodeling.

Posttranscriptional modification of retroviral primers is required for late stages of DNA replication

During reverse transcription of retroviral RNA, synthesis of (−) strand DNA is primed by a cellular tRNA that anneals to an 18-nt primer binding site within the 5′ long terminal repeat. For (+) strand synthesis using a (−) strand DNA template linked to the tRNA primer, only the first 18 nt of tRNA are replicated to regenerate the primer binding site, creating the (+) strand strong stop DNA intermediate and providing a 3′ terminus capable of strand transfer and further elongation. On model HIV templates that approximate the (−) strand linked to natural modified or synthetic unmodified tRNA3Lys, we find that a (+) strand strong stop intermediate of the proper length is generated only on templates containing the natural, modified tRNA3Lys, suggesting that a posttranscriptional modification provides the termination signal. In the presence of a recipient template, synthesis after strand transfer occurs only from intermediates generated from templates containing modified tRNA3Lys. Reverse transcriptase from Moloney murine leukemia virus and avian myoblastosis virus shows the same requirement for a modified tRNA3Lys template. Because all retroviral tRNA primers contain the same 1-methyl-A58 modification, our results suggest that 1-methyl-A58 is generally required for termination of replication 18 nt into the tRNA sequence, generating the (+) strand intermediate, strand transfer, and subsequent synthesis of the entire (+) strand. The possibility that the host methyl transferase responsible for methylating A58 may provide a target for HIV chemotherapy is discussed.

Distal enhancer regulation by promoter derepression in topologically constrained DNA in vitro

Long-range promoter–enhancer interactions are a crucial regulatory feature of many eukaryotic genes yet little is known about the mechanisms involved. Using cloned chicken βA-globin genes, either individually or within the natural chromosomal locus, enhancer-dependent transcription is achieved in vitro at a distance of 2 kb with developmentally staged erythroid extracts. This occurs by promoter derepression and is critically dependent upon DNA topology. In the presence of the enhancer, genes must exist in a supercoiled conformation to be actively transcribed, whereas relaxed or linear templates are inactive. Distal protein–protein interactions in vitro may be favored on supercoiled DNA because of topological constraints. In this system, enhancers act primarily to increase the probability of rapid and efficient transcription complex formation and initiation. Repressor and activator proteins binding within the promoter, including erythroid-specific GATA-1, mediate this process.

Direct sequencing of bacterial and P1 artificial chromosome-nested deletions for identifying position-specific single-nucleotide polymorphisms

A loxP-transposon retrofitting strategy for generating large nested deletions from one end of the insert DNA in bacterial artificial chromosomes and P1 artificial chromosomes was described recently [Chatterjee, P. K. & Coren, J. S. (1997) Nucleic Acids Res. 25, 2205–2212]. In this report, we combine this procedure with direct sequencing of nested-deletion templates by using primers located in the transposon end to illustrate its value for position-specific single-nucleotide polymorphism (SNP) discovery from chosen regions of large insert clones. A simple ampicillin sensitivity screen was developed to facilitate identification and recovery of deletion clones free of transduced transposon plasmid. This directed approach requires minimal DNA sequencing, and no in vitro subclone library generation; positionally oriented SNPs are a consequence of the method. The procedure is used to discover new SNPs as well as physically map those identified from random subcloned libraries or sequence databases. The deletion templates, positioned SNPs, and markers are also used to orient large insert clones into a contig. The deletion clone can serve as a ready resource for future functional genomic studies because each carries a mammalian cell-specific antibiotic resistance gene from the transposon. Furthermore, the technique should be especially applicable to the analysis of genomes for which a full genome sequence or radiation hybrid cell lines are unavailable.

The UNI3 Gene Is Required for Assembly of Basal Bodies of Chlamydomonas and Encodes δ-Tubulin, a New Member of the Tubulin Superfamily

We have cloned the UNI3 gene in Chlamydomonas and find that it encodes a new member of the tubulin superfamily. Although Uni3p shares significant sequence identity with α-, β-, and γ-tubulins, there is a region of Uni3p that has no similarity to tubulins or other known proteins. Mutant uni3–1 cells assemble zero, one, or two flagella. Pedigree analysis suggests that flagellar number in uni3–1 cells is a function of the age of the cell. The uniflagellate uni3–1 cells show a positional phenotype; the basal body opposite the eyespot templates the single flagellum. A percentage of uni3–1 cells also fail to orient the cleavage furrow properly, and basal bodies have been implicated in the placement of cleavage furrows in Chlamydomonas. Finally when uni3–1 cells are observed by electron microscopy, doublet rather than triplet microtubules are observed at the proximal end of the basal bodies. We propose that the Uni3 tubulin is involved in both the function and cell cycle-dependent maturation of basal bodies/centrioles.