DESIGN AND DEVELOPMENT OF THE AFRICAN PLASMODIUM FALCIPARUM DATABASE – (afriPFdb)

The detailed investigation of mantle structure from the dispersion of surface waves is a young but vigorous field of study. Observations have been accumulating rapidly in the past few years because of the wide-spread installation of long-period instruments. Modern methods of data analysis used in conjunction with high-speed digital computers have made it possible to determine dispersion with greater precision and over a broader spectrum than has previously been possible. Observations now extend out to the fundamental periods of free oscillations of the whole earth. Interpretation has lagged behind observation because of the difficulties inherent in the problem of dispersion over realistic models of a spherical earth. This problem is now well in hand and dispersion appropriate to the standard earth models suggested by earlier body waves studies has been calculated. Even with digital computers, however, the computations are so formidable that until recently only the most tentative efforts have been made to modify the standard earth structures to give a more satisfactory fit to the data. A review as recent as the one by Bolt in the preceding volume of this series was, of necessity, limited to a discussion of the various standard earth models with no attempt made to use the full power of surface waves as an independent technique. Recent developments have made detailed surface wave interpretations possible and new information, rather than generalized verification of old information, should be rapidly forthcoming. Project Mohole and the International Upper Mantle Project have focused the attention of many earth scientists on the upper mantle. Because of this renewed emphasis present information and speculation on the properties of the mantle based on a variety of sources is summarized and re-examined in some detail. This provides the guide-lines for potentially fruitful further research and points out the nature of some of the discrepancies and limitations in our present knowledge that may be resolved by the surface wave method

Integration of a polyomavirus recombinant containing highly repetitive sequence : analysis of the junctions and genome rearrangements

Studies on the integration of exogenous DNA into the genomes of mammalian cells have established that three different recombination mechanisms are involved; sites-pecific, illegitimate and homologous recombination. Since no essential functions have been found to be necessarily associated with the exogenous molecule it is beleived that this process faithfully reflects the natural recombination mechanisms of the cell. The DNA tumour virus paradigm has led to the development of a linear "replacement" model for integration by illegitimate recombination - model which predicts an excision of host DNA similar to the length of DNA inserted. RmI is a naturally occurring thermosensitive Py recombinant that contains an insertion (INS) of mouse cellular DNA. RmI should have the potential to integrate by any or all three of site-specific, illegitimate, or homologous recombination mechanisms. Firstly, RmI contains viral Py sequences known to integrate by illegitimate recombination. Secondly, RmI contains B2 and MT repetitive sequences both of which have 100,000 homologous copies dispersed throughout the rat genome any one of which could serve as a target for homologous integration. Finally the junctions between Ins and the Py sequences of RmI display features that suggest that RmI may be capable of site-specific recombination. My previous work on the integration of RmI into the genomes of rat cells showed that at the temperature non-permissive for replication, integration was non random with respect to the sequences of RmI. One region of RmI was underrepresented, whereas two regions, including the region of Ins containing the repetitive elements B2 and MT, were significantly overrepresented. Furthermore, the lengths of the integrated genomes tended importantly toward the unit length of RmI contrary to what was observed at the permissive temperature. In an effort to further define the integration mechanism and in particular to determine the nature of the viral-cellular junctions at the molecular level as well as to characterize the host site before and after integration, the cellular DNAs flanking 6 junctions from 3 transformed cell lines were cloned (4 in this study, 2 were previously cloned) and the sequences across 4 of these junctions were determined (one previously determined, 3 were determined here). The cloned DNAs were used to map the rearrangements of the cellular DNA caused by the integration of RmI. Furthermore, the fate of the rearranged intervening host sequences in one of the clones was determined. The results show that the overrepresentation of the repetitive sequences was due to their acting as hotspots for illegitimate recombination. Even though the host genome contained over 105 potential targets for homologous recombination we found no evidence for homologous integration, and conclude that it is not an efficient procedure in the case of RmI. Furthermore, contrary to previous reports which suggested that exogenous DNA integrated preferentially into repetitive sequences of the host, we found that the DNA flanking all but one junction was unique sequence DNA. Even though RmI was transfected in the presence of carrier DNA, the results presented here show that it integrated directly into the rat cellular DNA. This shows that transgenomes are not necessary intermediates for the integration of (circular) DNA even when transfected in the presence of carrier. The minimum lengths of the rearrangements caused to the host DNA by RmI's integration into two of the clones was determined to be 12 kbp for an insertion of 7 kbp and 55 kbp for an insertion of 6 kbp. It was further established that the intervening host DNA in the latter clone had been deleted. We show (for the first time by hybridization) that in the case of the third clone the DNAs flanking the insertion on either side were linked before integration. The rearrangement caused by RmI's integration is complex but can be partially explained by an inversion event of approximately 20 kbp for an insertion of 7 kbp. The length and nature of the rearrangements are incompatible with a linear insertion-replacement model, and are more easily explained by an integration mechanism in which the incoming exogenous DNA recombines with a looped structure of chromosomal DNA. Such a model, which takes into account recent findings on chromatin structure, is presented

Análise de tripletos e de repetições em estruturas primárias de DNA

Doutoramento em Engenharia InformáticaO desenvolvimento de equipamentos de descodificação massiva de genomas veio aumentar de uma forma brutal os dados disponíveis. No entanto, para desvendarmos informação relevante a partir da análise desses dados é necessário software cada vez mais específico, orientado para determinadas tarefas que auxiliem o investigador a obter conclusões o mais rápido possível. É nesse campo que a bioinformática surge, como aliado fundamental da biologia, uma vez que tira partido de métodos e infra-estruturas computacionais para desenvolver algoritmos e aplicações informáticas. Por outro lado, na maior parte das vezes, face a novas questões biológicas é necessário responder com novas soluções específicas, pelo que o desenvolvimento de aplicações se torna um desafio permanente para os engenheiros de software. Foi nesse contexto que surgiram os principais objectivos deste trabalho, centrados na análise de tripletos e de repetições em estruturas primárias de DNA. Para esse efeito, foram propostos novos métodos e novos algoritmos que permitirem o processamento e a obtenção de resultados sobre grandes volumes de dados. Ao nível da análise de tripletos de codões e de aminoácidos foi proposto um sistema concebido para duas vertentes: por um lado o processamento dos dados, por outro a disponibilização na Web dos dados processados, através de um mecanismo visual de composição de consultas. Relativamente à análise de repetições, foi proposto e desenvolvido um sistema para identificar padrões de nucleótidos e aminoácidos repetidos em sequências específicas, com particular aplicação em genes ortólogos. As soluções propostas foram posteriormente validadas através de casos de estudo que atestam a mais-valia do trabalho desenvolvido.The development of massive genome decoding equipment has increased available data tremendously. Nevertheless, increasingly more specific software is required to bring to light the relevant information from all of that data. The software must be oriented towards certain tasks which assist the researcher in reaching conclusions as quickly as possible. Thus, the field of bioinformatics appears as a fundamental ally of biology, taking advantage of computational methods and infrastructures to develop computer algorithms and applications. On the other hand, in most cases due to new biological issues, it is necessary to respond with specific new solutions. Therefore, developing applications is a permanent challenge for software engineers. It was in this context that the main aims of this work emerge. They are focused on analyzing triplets and repetitions in primary DNA structures. To this end, new methods and new algorithms were proposed to allow results to be processed and obtained from large volumes of data. A system was designed for two strands of analysis terms of codon triplets and amino acids. On the one hand it processes data; on the other hand, it makes the processed data available on the Web through a query builder mechanism. As for analyzing repetitions, a system to identify repeated nucleotide and amino acid patterns in specific sequences was proposed and developed, particularly applied to orthologous genes. The solutions found were later validated through case studies which attested the value of the contribution this work has made

Deep molecular phylogeny of the Pterygota

[no abstract