Molecular and Cell Biology of Infantile (CLN1) and variant Late Infantile (CLN5) Neuronal Ceroid Lipofuscinoses

Myös verkossa; väitöskirja, ohj. Leena Peltonen-Paloti

Molecular and cell biology of infantile (CLN1) and variant late infantile (CLN5) neuronal ceroid lipofuscinoses

Myös verkossa; väitöskirja, ohj. Leena Peltonen-Paloti

COMPARATIVE GENOMICS AND MOLECULAR EVOLUTION: NEW GENOMIC RESOURCES FOR THE HYMENOPTERA AND EVOLUTIONARY STUDIES ON THE GENES OF THE \u3ci\u3eNasonia vitripennis\u3c/i\u3e HOX COMPLEX.

Research on insects, the most successful group from all metazoans on earth, has important societal, as well as scientific benefits. Insects occupy a wide range of roles, which have an effect on human life either because the former pose serious threats to public health and commercial crops as well as in some cases represent the only way to propagate food resources. Despite their tremendous importance, insect genomics remained an uneven territory dominated by studies in the Drosophila group and the mosquitoes. This dissertation attempts to: 1) report on advances in the development and characterization of genomic tools for species of the order Hymenoptera in the hopes of helping to close this gap; and 2) to shed light on the organization, origin and evolution of genes of the Hox cluster in species of the order Hymenoptera through molecular evolution analyses that were possible thanks to the availability of the aforementioned genomic resources

Rendering the Unseen Virome Visible

Thousands of distinct viruses have been discovered and have had their genomes sequenced. Despite, or perhaps because of this, the concept of “viruses” remains fluid. No gene or gene family is conserved between viruses, making them “polyphyletic.” What makes a genetic element a virus? How many kinds of viruses exist? When a new genetic element is discovered, how can one determine if it is a virus? These questions are complicated, and further experimentation to explore the "virus sequence space" will be required. Both genetic interpretation and modeling of important virus genes as well as isolation and analysis of virus particles can lead us through the vast diversity of the virus sequence space, and maybe allow us to "touch the walls" at the extremes of this space. Ultimately, these considerations will aid us in answering more practical questions. For example, how do the multitudes of viruses living in and on us affect our well-being? This dissertation presents original research that pushes the field of virology forward by striking out into the unexplored reaches of the virus sequence space, expanding our knowledge of virus genome sequences, i.e. the virome. Orthogonal techniques are developed and implemented to latch on to and explore distinctive virus-like signals, including protection of virus genomes from nucleases, circular DNA molecules, and three-dimensional structure conservation of capsids and other virion proteins. Additionally, the development and public release of a bioinformatic tool, Cenote-Taker2, addresses the persistent problems of finding familiar and divergent virus sequences of "known types" in complex datasets and accurately annotating these sequences for distribution to the scientific public. This should accelerate research across the field of virology. Finally, in the last chapter, sequencing data from thousands of human metagenomes is interrogated to pull out high-quality sequences from over 80,000 virus taxa, and strong associations are defined between over a thousand of these virus taxa and a variety of human chronic disease states

Taxonomic and functional analysis of metagenomes

Dissertação de mestrado em BioinformáticaOver the years, metagenomics has demonstrated to play an essential role on the study of the microorganisms that live in microbial communities, particularly those who inhabit the human body. Several bioinformatic tools and pipelines have been developed, but usually they only address one question: "Who is there?" or "What are they doing?". This work aimed to develop a computational framework to answer the two questions simultaneously, that is, perform a taxonomic and functional analysis of microbial communities. Merlin, a previously developed software designed for the construction of genome-scale metabolic models for single organisms, was extended to deal with metagenomics data. It has an userfriendly and intuitive interface, not requiring command-line knowledge and further libraries dependencies or installation, as many other tools. The extended version of Merlin can predict the taxonomic composition of an environmental sample based on the results of homology searches, where the proportions of phyla and genera present are discriminated. Regarding the metabolic analysis, it allows to identify which enzymes are present and calculate their abundance, as well as to nd out which metabolic pathways are e ectively present. The performance of the tool was evaluated with samples from the Human Microbiome Project, particularly from the saliva. The taxonomic membership predicted in Merlin was in agreement with other tools, despite some di erences in the proportions. The functional characterization showed a conserved pool of pathways through di erent samples, although Merlin sometimes presented less pathways than expected because the routine is highly dependent on the enzymes annotation. Overall, the results showed the same pattern as reported before: while the pathways needed for microbial life remain relatively stable, the community composition varies extensively among individuals. In the end, Merlin demonstrated to be a reliable standalone alternative to web services for those scientists that have concerns about sharing data.Ao longo dos anos, a metagenómica demonstrou ter um papel essencial no estudo dos microorganismos que vivem em comunidades bacterianas, particularmente aqueles que habitam o corpo humano. Várias ferramentas e pipelines bioinformáticas foram desenvolvidas, mas normalmente estas apenas abordam uma destas questões: "Quem está lá?" ou "O que é que estão a fazer?" Este trabalho teve como objectivo o desenvolvimento duma ferramenta computacional para responder aos dois problemas em simultâneo, isto é, realizar tanto uma análise taxonómica como funcional de comunidades microbianas. O Merlin, um software anteriormente desenvolvido para construir modelos metabólicos à escala genómica para um organismo, foi estendido para tratar dados de metagenómica. O programa possui uma interface intuitiva e amiga do utilizador, não necessitando de conhecimentos de linha de comandos nem de dependências de bibliotecas ou instalação de aplicações adicionais. Esta versão estendida do Merlin prevê a composição taxonómica global dum metagenoma baseado nos resultados de procuras de sequências homólogas, onde as proporções dos fila e géneros são apresentadas. No que diz respeito à análise metabólica, o Merlin permite identificar quais as enzimas presentes e calcular a sua abundância, bem como identificar quais as vias metabólicas que estão efectivamente presentes. O desempenho da ferramenta foi avaliado com amostras do Projecto do Microbioma Humano, particularmente com amostras da saliva. A composição taxonómica prevista no Merlin esteve de acordo com outras ferramentas, apesar de algumas diferenças observadas nas proporções. A caracterização funcional mostrou um conjunto conservado de vias metabólicas nas diferentes amostras, mesmo que o Merlin tenha identificado menos enzimas que o esperado, pois o método é bastante dependente do processo anotação. Globalmente, os resultados revelaram o mesmo padrão reportado anteriormente: enquanto as vias metabólicas necessárias para a vida microbiana se mantêm estáveis, a composição taxonómica varia bastante entre indivíduos. No final, o Merlin demonstrou ser uma alternativa fidedigna a serviços web para aqueles cientistas que têm restrições em divulgar os seus dados não publicados num website.Fundação para a Ciência e a Tecnologia (FCT) - Projeto COMPETE FCOMP-01-0124-FEDER-015079.ERDF - European Regional Development Fund atrav es do programa COMPETE (programa operacional para a competitividade)

The Proximon: Representation, Evaluation, and Applications of Metagenomic Functional Interactions

The effective use of metagenomic functional interactions represents a key prospect for a variety of applications in the field of functional metagenomics. By definition, metagenomic operons represent such interactions but many operon predictions protocols rely on information about orthology and/or gene function that is frequently unavailable for metagenomic genes. In this thesis, I introduce the proposition of the proximon as a unit of functional interaction that is intended for use in metagenomic scenarios where supplemental information is sparse. The proximon is defined as a series of co-directional genes where minimal intergenic distance exists between any two consecutive member genes within the same proximon. In particular, the proximon is presented here as a biological abstraction aimed at facilitating bioinformatics and computational goals. In this thesis, proximons are constructed as information theoretic entities and employed in a variety of contexts related to functional metagenomics. I begin by implementing a computational representation for proximon data and demonstrate its utility through the deployment of a public database. Next, I perform a formal validation where proximons are contrasted against known operons by using the Escherichia coli K-12 model organism as a gold standard to measure the extent to which proximons emulate actual operons. This is followed by a demonstration of how proximon data can be applied to infer potential functional networks and depict potential functional modules. I conclude by enumerating the limitations of the research performed here and I present objectives and goals for future work