The human genome is predicted to contain ~20,500 protein-coding genes. The encoded proteins are the key players in the body, but the functions and localizations of most proteins are still unknown. Antibody-based proteomics has great potential for exploration of the protein complement of the human genome, but there are antibodies only to a very limited set of proteins. The Human Proteome Resource (HPR) project was launched in August 2003, with the aim to generate high-quality specific antibodies towards the human proteome, and to use these antibodies for large-scale protein profiling in human tissues and cells. The goal of the work presented in this thesis was to evaluate if antigens can be selected, in a high-throughput manner, to enable generation of specific antibodies towards one protein from every human gene. A computationally intensive analysis of potential epitopes in the human proteome was performed and showed that it should be possible to find unique epitopes for most human proteins. The result from this analysis was implemented in a new web-based visualization tool for antigen selection. Predicted protein features important for antigen selection, such as transmembrane regions and signal peptides, are also displayed in the tool. The antigens used in HPR are named protein epitope signature tags (PrESTs). A genome-wide analysis combining different protein features revealed that it should be possible to select unique, 50 amino acids long PrESTs for ~80% of the human protein-coding genes. The PrESTs are transferred from the computer to the laboratory by design of PrEST-specific PCR primers. A study of the success rate in PCR cloning of the selected fragments demonstrated the importance of controlled GC-content in the primers for specific amplification. The PrEST protein is produced in bacteria and used for immunization and subsequent affinity purification of the resulting sera to generate mono-specific antibodies. The antibodies are tested for specificity and approved antibodies are used for tissue profiling in normal and cancer tissues. A large-scale analysis of the success rates for different PrESTs in the experimental pipeline of the HPR project showed that the total success rate from PrEST selection to an approved antibody is 31%, and that this rate is dependent on PrEST length. A second PrEST on a target protein is somewhat less likely to succeed in the HPR pipeline if the first PrEST is unsuccessful, but the analysis shows that it is valuable to select several PrESTs for each protein, to enable generation of at least two antibodies, which can be used to validate each other. / QC 20100705

The desert ant Cataglyphis fortis lives in the Sahara desert where it is exposed to extreme temperatures up to 70° C. In other words, the organism is considered as a thermophile. Until now the genome remains unknown but the fact that C. fortis provides heat stable proteins makes it very interesting in the field of protein studies and maybe even therapeutical research later on. This thesis focuses on trying to find genes that are expressed in C. fortis. Different genes were chosen and capable primers designed. After fishing for the enzyme GAPDH a fragment was found and sequenced. The sequence showed 31% homology on amino acid level with protein disulfide isomerase (PDI) in Apis mellifera (honey bee) and Drosophila melanogaster (fruitfly). The received sequence can be used to design new primers that match exactly. Gene fishing can also be continued by using the other primers that were designed during this project.

Exons are expression DNA sequences. A DNA sequence which includes gene has exons and introns. During transcription and translation, introns will be removed, and exons will remain to become protein. Many researchers need exon primers for PCR experiments. However, it is a difficult to find that many exon primers satisfy all primer design constraints at the same time. Here, we proposed an efficient exon primer design algorithm. The algorithm applies multiobjective genetic algorithm (MGA) instead of the single objective algorithm which can easily lend to unsuitable solutions. And a hash-index algorithm is applied to make specificity checking in a reasonable time. The algorithm has tested by a variety of mRNA sequences. These dry dock experiments show that our proposed algorithm can find primers which satisfy all exon primer design constraints.

In polymerase chain reaction (PCR), in order to amplify massive DNA sequences successfully, it needs to design an appropriate primer pair. The constraints derived from the traits of PCR for proceeding PCR are used in searching for primer pairs. In this paper, in order to decrease the searching space and to increase the feasible quality of primers, a double orthogonal arrays intelligent crossover genetic algorithm (DOAIGA) is used to solve the primer design problem. DOAIGA combines the traditional genetic algorithm and the Taguchi methodology to efficiently search feasible primers under required constraints. The proposed intelligent crossover subsystem mainly concentrates on the better genes more systematic. The key point of DOAIGA is to achieve the elitism goal by applying the orthogonal arrays (OAs) that is used in quality engineering with a small amount of experiment features. In this thesis, the double orthogonal arrays are used to approach a better forward and reverse primers separately. Compared to the current existing softwares, DOAIGA can obtain feasible primer pairs more effectively. Finally the correctness of primer pair is verified by PCR experiment.

The patch reefs located in Biscayne National Park (BNP) are some of the most northern reefs of the Florida reef system. The focus of my study is seven patch reefs that were first surveyed annually between 1977 and 1981, revealing 8% - 28% cover by scleractinian corals. An assessment of BNP patch reefs completed in 2000 reported that coral cover had decreased to approximately 0.4% - 10%. The once dominant species in the Florida reef tract, Acropora palmata and A. cervicornis, have rapidly declined over time and were not found in any transects during the 2000 survey. This study is a re-assessment of the BNP patch reefs surveyed in 1977-1981. In addition, one patch reef from BNP and three in upper keys region of the Florida Keys National Marine Sanctuary (FKNMS) have been included (a total of 11 patch reefs, all with historical data available). This study found 2% - 13% coral cover at these 11 reefs using a photographic survey (Point Count) and 4% - 21% coral cover using Atlantic and Gulf Rapid Reef Assessment (AGRRA) survey methods. These results are relatively similar to results reported for the same patch reefs in the 1990s and in 2002, indicating that the major changes occurred earlier with the extreme decline in Acropora spp. Montastraea annularis complex cover has also declined substantially at the BNP sites from 5.4% in 1977-81 to 1.3% in 2009. Although the number of species recoded on the seven resurveyed BNP patch reefs was only 23, compared with 28 recorded in the 1977-81 study, all species are still present in the region surveyed, indicating no actual loss of over all species richness.

No description available.

L'objectiu principal del nostre estudi ha estat, en primer lloc, fer una "història de la lògica" que abastés el període que va aproximadament des de mitjans del segle XIX, època en què Boole i De Morgan renoven la lògica tradicional, fins als anys vint del segle passat, quan la lògica de primer ordre es consolida com el llenguatge lògic "par excellence" i la concepció model-teorètica s'obre camí de forma inexorable. Segonament, el nostre objectiu ha estat fer un estudi comparatiu de les contribucions del corrent algèbric i logicista a la gènesi i desenvolupament de la lògica contemporània, particularment de la lògica de primer ordre i de la concepció model-teorètica predominant avui en dia. Al nostre parer, el naixement i desenvolupament de la lògica contemporània ha anat de bracet amb les recerques sobre els fonaments de les matemàtiques dutes a terme en el període estudiat, per la qual cosa el nostre objectiu ha estat finalment fer-nos ressó de l'estret lligam entre els problemes relatius a la fonamentació de les matemàtiques i les recerques lògiques pròpiament dites. D'acord amb tot l'anterior, hem dividit la nostra memòria en tres parts. Les dues primeres parts les hem dedicades respectivament a l'estudi del desenvolupament de la tradició algèbrica i logicista i estan dividides en diferents capítols, dedicat cada un d'ells als autors més representatius d'aquestes dos corrents: Boole, Peirce i Schröder, d'una banda, i Dedekind, Frege i Russell de l'altra. Finalment, la tercera part l'hem dedicada als desenvolupaments més importants que seguiren la publicació de l'obra de Whitehead i Russell Principia Mathematica (1910-1913) i que més influència tingueren, des del nostre punt de vista, en el desenvolupament posterior de la lògica, a saber, les recerques de Hilbert i la seva escola sobre l'aplicació del mètode axiomàtic a les diferents branques de les matemàtiques i, en particular, a la lògica, i les recerques model-teorètiques de Löwenheim i Skolem sobre el fragment de primer ordre de la lògica de relatius. Aquestes recerques tingueren efectivament una influència cabdal en la gènesi i desenvolupament de la lògica de primer ordre i la concepció model-teorètica predominant avui en dia, per la qual cosa el seu estudi presenta un indubtable interès històric i dóna, a més, una bona mesura de les contribucions de les tradicions algèbrica i logicista a la lògica contemporània i, en particular, de les limitacions que presenten en aquest sentit ambdues tradicions. Entre les contribucions més destacades del nostre estudi per tal de determinar quines han estat les aportacions dels diferents autors estudiats a la gènesi i desenvolupament de la lògica contemporània i la moderna concepció semàntica de la mateixa cal destacar, entre d'altres, l'estudi realitzat sobre l'evolució de la lògica de relatius i la lògica quantificacional -de primer i segon ordre- en l'obra de Peirce, l'estudi sobre les definicions dels principals conceptes semàntics -interpretació, conseqüència lògica, independència, etc.- en l'obra de Schröder, l'estudi sobre la gènesi i evolució del logicisme fregeà a partir de la seva tesi de doctorat (1873) i la seva Habilitationschrift (1874), una interpretació de la teoria ramificada de tipus de Russell que no és l'habitual en la historiografia clàssica (Copi, Quine, Kneale i Kneale et alia), l'estudi de la connexió de la problemàtica tractada en els escrits de Löwenheim i Skolem amb el programa de recerca iniciat per Peirce i Schröder i, finalment, l'estudi de l'evolució en el si de l'escola de Hilbert d'algunes de les idees bàsiques de la lògica contemporània i la moderna concepció model-teorètica de la mateixa a partir de l'estudi de les lliçons (inèdites) impartides per Hilbert a Göttingen els cursos de 1905 i 1917-18. / As its title indicates, this work intends to make a historical itinerary by some of the main developments that took place in the field of logic and the foundations of the mathematics between the second half of the 19th century and the first fourth of the 20th century approximately. Moreover, it pretends also to make a comparative study of the development of the algebraic and logicist traditions in this period that allows to gauge the contributions of each one of them to the genesis and development of contemporary logic and the modern model-theoretic conception of it. With this aim, the most highlighted contributions of our work are, among others, the study carried out about the evolution and relationship of the logic of relatives and quantificational logic -of first and second order- in Peirce's work, the research into the definitions of the main semantic concepts -interpretation, logical consequence, independence, etc- in Schröder's work, the study of the genesis and evolution of fregean logicism from his doctorate thesis (1873) and his "Habilitationschrift" (1874), an interpretation of Russell's theory of types which it is unusual in the classical historiography, the research into the connection of the problems treated in Löwenheim and Skolem writings with the program of research pioneered by Peirce and Schröder and, finally, the study of the evolution in the bosom of Hilbert's school of some of the main ideas of contemporary logic and metalogic from the study of the lessons (unedited) imparted by Hilbert in Göttingen in the courses of 1905 and 1917-18.

Freie Universiẗat, Diss., 2006--Berlin. / Dateiformat: zip, Dateien im PDF-Format.

Este estudo possui o interesse em ampliar as discussões, no campo da história da educação, sobre o uso de cartilhas como dispositivos por meio dos quais se procurou pôs em circulação, no espaço escolar, os ideais higiênicos, cuja aquisição permitiria a construção de uma vida vista como saudável e feliz. As cartilhas analisadas são: Cartilha de Higiene, de 1922, de Antônio de Almeida Júnior, médico e educador, conhecido por ter tido envolvimento no Movimento da Escola Nova; e Cartilha de Higiene, de 1936, de Renato Kehl, médico e defensor da eugenia no Brasil. As obras em questão foram produzidas em um cenário em que proliferaram intervenções oriundas do campo médico, entre outros campos científicos, com vistas à conformação da sociedade brasileira em bases modernas. Pretende-se analisar esses livros, valorizando sua dimensão de objeto cultural, explorando o caráter prescritivo de que se revestem, dirigido às crianças, em vários aspectos de sua vida escolar e doméstica, e ainda as representações produzidas sobre infância, família, escola e saúde. / This study has the interest in broadening discussions in the field of history education, on the use of booklets as devices through which sought to put into circulation, in the school space, hygienic ideals, whose acquisition would allow the construction of a life viewed as healthy and happy. The primers are analyzed: Primer, hygiene of 1922, Antônio de Almeida Júnior, doctor and educator, known to have had involvement in the movement of the new school; and Primer, hygiene of 1936, Renato Kehl, doctor and proponent of eugenics in Brazil. The works in question were produced in a scenario in which proliferated interventions from the medical field, among other scientific fields, with a view to the formation of the Brazilian society in modern bases. We intend to analyze these books, valuing its dimension of cultural object, exploring the prescriptive character that are directed at children, in various aspects of their school life and home, and still the representations produced about childhood, family, school and health.

Orientadora: Janete Apparecida Desidério / Banca: Agda Paula Facincani / Banca: Irlan Leite de Abreu / Resumo: Como uma alternativa para diminuir as agressões constantes que o ecossistema vem sofrendo, devido à grande quantidade de produtos químicos utilizados no controle de pragas, pesquisas envolvendo microrganismos capazes de promover o controle biológico tem se intensificado. Dentre estes microrganismos a bactéria Bacillus thuringiensis tem se destacado. Essa bactéria caracteriza-se pela produção de proteínas tóxicas a representantes de diversas ordens de insetos. Em particular, as proteínas Vip3A, estão em amplo estudo devido a sua especificidade, alto potencial ativo e como alternativa para o controle da resistência de insetos às proteínas Cry. Diante disto, o objetivo deste trabalho foi selecionar, a partir de 1080 isolados de diferentes regiões brasileiras, aqueles portadores de genes vip3A e obter a sequência de nucleotídeos completa dos mesmos. As linhagens padrão B. thuringiensis var. kurstaki HD1, B. thuringiensis var. tolworthi HD125 e o isolado I187 tiveram seus DNAs amplificados com oligonucleotídeos baseados na sequência de genes vip3A, descritos no banco de dados de B. thuringiensis e, a partir dos amplicons obtidos, a sequência completa de nucleotídeos dos mesmos foi determinada, utilizando-se da estratégia de "primer walking". A proteína Vip3Aa43 (GenBank: [HQ594534]) da linhagem HD1 demonstrou ser 100% idêntica às proteínas Vip3Aa já descritas. Já as proteínas Vip3Aa42 (GenBank: [HQ587048]) da linhagem HD125 e Vip3Ag5 (GenBank: [HQ542193]) do isolado I187 demonstraram similaridade de 99% com as proteínas descritas Vip3Aa35 e Vip3Ag2, respectivamente, demonstrando serem duas novas proteínas Vip3A, devido às substituições de aminoácidos ocorridas. Os três genes vip3A obtidos poderão ser utilizados na produção de plantas Bt, piramidadas ou não, visando ao manejo da resistência dos insetos praga / Abstract: As an alternative to decrease the constant aggressions that the ecosystem has suffered due to the large amount of chemical products used in pest control, researches involving microorganisms able to promoting biological control have been intensified. Among these microorganisms the bacterium Bacillus thuringiensis has been stood out. This bacterium is characterized by the production of toxic proteins to representatives of several insect orders. In particular, the Vip3A proteins are in large study due to its specificity, and high active potential as an alternative to control of insect's resistance to Cry proteins. According to this, the aim of this work was to select from 1080 isolates in different Brazilian regions, those carrying vip3A genes and obtain the complete nucleotide sequence of the same. The standard strains B. thuringiensis var. kurstaki HD1, B. thuringiensis var. tolworthi HD125 and the isolate I187 had their DNA amplified with primers based on vip3A gene sequence described in database of B. thuringiensis, and from the amplicons obtained, the full sequence of nucleotides was determined, by the use of the strategy of "primer walking". The protein Vip3Aa43 (GenBank: [HQ594534]) of HD1 strain showed to be 100% identical to Vip3Aa proteins already described. However, the proteins Vip3Aa42 (GenBank: [HQ587048]) of HD125 strain and Vip3Ag5 (GenBank: [HQ542193]) of the isolate I187 showed 99% similarity with the Vip3Aa35 and Vip3Ag2 proteins described, respectively, showing been two new Vip3A proteins due to amino acid substitutions occurred. The three vip3A genes obtained can be used in the production of Bt crops, pyramidal or not, aiming to resistance management of pest insects / Mestre