Chromosome Descrambling Order Analysis in ciliates

Ciliates are a type of unicellular eukaryotic organism that has two types of nuclei within each cell; one is called the macronucleus (MAC) and the other is known as the micronucleus (MIC). During mating, ciliates exchange their MIC, destroy their own MAC, and create a new MAC from the genetic material of their new MIC. The process of developing a new MAC from the exchanged new MIC is known as gene assembly in ciliates, and it consists of a massive amount of DNA excision from the micronucleus, and the rearrangement of the rest of the DNA sequences. During the gene assembly process, the DNA segments that get eliminated are known as internal eliminated segments (IESs), and the remaining DNA segments that are rearranged in an order that is correct for creating proteins, are called macronuclear destined segments (MDSs). A topic of interest is to predict the correct order to descramble a gene or chromosomal segment. A prediction can be made based on the principle of parsimony, whereby the smallest sequence of operations is likely close to the actual number of operations that occurred. Interestingly, the order of MDSs in the newly assembled 22,354 Oxytricha trifallax MIC chromosome fragments provides evidence that multiple parallel recombinations occur, where the structure of the chromosomes allows for interleaving between two sections of the developing macronuclear chromosome in a manner that can be captured with a common string operation called the shuffle operation (the shuffle operation on two strings results in a new string by weaving together the first two, while preserving the order within each string). Thus, we studied four similar systems involving applications of shuffle to see how the minimum number of operations needed to assemble differs between the types. Two algorithms for each of the first two systems have been implemented that are both shown to be optimal. And, for the third and fourth systems, four and two heuristic algorithms, respectively, have been implemented. The results from these algorithms revealed that, in most cases, the third system gives the minimum number of applications of shuffle to descramble, but whether the best implemented algorithm for the third system is optimal or not remains an open question. The best implemented algorithm for the third system showed that 96.63% of the scrambled micronuclear chromosome fragments of Oxytricha trifallax can be descrambled by only 1 or 2 applications of shuffle. This small number of steps lends theoretical evidence that some structural component is enforcing an alignment of segments in a shuffle-like fashion, and then parallel recombination is taking place to enable MDS rearrangement and IES elimination. Another problem of interest is to classify segments of the MIC into MDSs and IESs; this is the second topic of the thesis, and is a matter of determining the right "class label", i.e. MDS or IES, on each nucleotide. Thus, training data of labelled input sequences was used with hidden Markov models (HMMs), which is a well-known supervised machine learning classification algorithm. HMMs of first-, second-, third-, fourth-, and fifth-order have been implemented. The accuracy of the classification was verified through 10-fold cross validation. Results from this work show that an HMM is more likely to fail to accurately classify micronuclear chromosomes without having some additional knowledge

Models of natural computation : gene assembly and membrane systems

This thesis is concerned with two research areas in natural computing: the computational nature of gene assembly and membrane computing. Gene assembly is a process occurring in unicellular organisms called ciliates. During this process genes are transformed through cut-and-paste operations. We study this process from a theoretical point of view. More specifically, we relate the theory of gene assembly to sorting by reversal, which is another well-known theory of DNA transformation. In this way we obtain a novel graph-theoretical representation that provides new insights into the nature of gene assembly. Membrane computing is a computational model inspired by the functioning of membranes in cells. Membrane systems compute in a parallel fashion by moving objects, through membranes, between compartments. We study the computational power of various classes of membrane systems, and also relate them to other well-known models of computation.Netherlands Organisation for Scientific Research (NWO), Institute for Programming research and Algorithmics (IPA)UBL - phd migration 201

Use of microbiome data to explain the expression of productive traits in domestic species

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Veterinaria, leída el 11-03-2022El descubrimiento de comunidades microbianas asociadas simbióticamente a organismos eucariotas ha llevado a un cambio de paradigma en la definición de individuo biológico, que ahora se ve como una combinación codependiente del hospedador y su microbioma, u holobionte. Por tanto, el estudio de los microbiomas se ha convertido en algo fundamental para comprender la biología de los organismos vivos complejos. De hecho, se ha observado que las comunidades microbianas poseen un papel crucial en la salud, supervivencia, desarrollo y metabolismo del hospedador. Los recientes avances en secuenciación genética han supuesto un importante impulso para la investigación en microbiología, al permitir la obtención de bases de datos de secuenciación masiva que abarcan una gran parte de la diversidad presente dentro de los microbiomas. La era del next-generation sequencing ha aportado nuevos conocimientos sobre el efecto de las comunidades microbianas sobre el fenotipo del hospedador, con especial relevancia del microbioma intestinal. Para la industria ganadera este hecho ha dado lugar a importantes avances en la comprensión de los mecanismos biológicos que influyen en productividad, sostenibilidad y bienestar animal, lo que podría ser útil para afrontar los desafíos existentes en este sector...The discovery of microbial communities symbiotically associated with eukaryotic organisms has led to a paradigm shift in the definition of the biological individual, which is now seen as a co-dependent combination of the host and its microbiome, or holobiont. Thus, the study of microbiomes has become essential to understand the biology of complex living organisms. Indeed, current research points to a crucial role of microbial communities in host health, survivability, development and metabolism. Recent advances in DNA sequencing have entailed a significant boost to microbial research, allowing the generation of massive sequencing databases encompassing a large proportion of the diversity inside microbiomes. The era of next-generation sequencing has brought new knowledge about the role of microbial communities, with special significance for gut microbiomes, in host phenotype. For livestock industry, this has led to important advances in the understanding of biological mechanisms influencing animal welfare, productivity and sustainability, which could be useful to face existing challenges in animal production...Fac. de VeterinariaTRUEunpu

EVOLUTION OF WOLBACHIA SYMBIOSIS IN ARTHOPODS AND NEMATODES: INSIGTHS FROM PHYLOGENETICS AND COMPARATIVE GENOMICS

Wolbachia is a bacterium observed in relationship with a wide array of arthropod and nematode species. This is an obligate intracellular symbiont, maternally transferred through the host oocytes. In arthropods Wolbachia is able to manipulate reproduction, using multiple strategies to increase the fitness of infected females. In nematodes the bacterium has a fundamental, and not completely understood, role in larvae development. Wolbachia infects ~50% of all the arthropod species worldwide, and in some of them it can be considered the most important sex determination factor. In contrast, Wolbachia presence is much more limited in nematodes, being present in a limited number of filarial species. The taxonomic status within the Wolbachia genus is highly debated, with the current classification dividing all strains in 14 'supergroups'. During my Ph.D. I studied the evolution of the symbiotic relationship between Wolbachia and its arthropod and nematode hosts, using genomic approaches. Indeed, during the evolution of the Wolbachia-host relationship, genetic signs have been left in the Wolbachia genomes. I worked to identify these genomic signs and to evaluate them within an evolutionary frame, in order to obtain a better understanding of how the Wolbachia-host symbiosis evolved. The work here presented can be organized in three major sections: i) the sequencing and analysis of the genome of the filarial nematode Dirofilaria immitis and of its symbiotic Wolbachia strain, wDi; ii) the sequencing of the genome of Wolbachia endosymbiont of Litomosoides sigmodontis, and the phylogenomic reconstruction of the Wolbachia supergroups A-D; iii) a comparison of the genomes of 26 Wolbachia strains spanning the A to F supergroups. Here a schematic summary of the results is reported: 1. Dirofilaria immitis and the Wolbachia symbiont wDi show metabolic complementarity for fundamental pathways 2. The metabolic pathway for the synthesis of wDi membrane proteins is one evolving the fastest in the genome of the bacterium 3. Nematode Wolbachia belonging to supergroups C and D are monophyletic, indicating that a single transition to mutualism likely occurred during the evolution of Wolbachia 4. Wolbachia strains of the C supergroup show genomic features that are unique in the genus, such as a much higher level of synteny compared to the rest of Wolbachia supergroups, and a newly generated pattern of GC skew curves, typically observed in free-living bacteria genomes 5. Wolbachia supergroups show conserved genomic features, which suggest genomic isolation among them

Eukaryotic Microbes in the Deep Sea: Abundance, Diversity, and the Effect of Pressure

The dark ocean is vast, high in pressure, cold, and scarce in resources, but has been shown to support a diverse and active microbial community wherever it is studied. Such studies, however, are scarce due to the difficulty of sampling at such depths, and are difficult to interpret due to compounding effects of pressure and temperature on physiology. Protists, functionally defined as the microbial portion of the domain Eukarya, are particularly neglected in studies of deep-sea microbiology. Here, I present three studies on microbial eukaryotes in the deep sea: first, a study of the abundance of microbial eukaryotes in the deep sea, second, a quantitative approach to study broad-scale diversity in the deep sea; and last, a series of experiments to explore the effect of deep-sea conditions on surface-isolated flagellates. In the deep sea, I found that eukaryote abundances decrease much more sharply than prokaryote abundances with depth, though most of this decrease occurs in the upper 1000 m, below which eukaryote abundance is relatively constant. In water masses below 1000 m, 50-70% of total eukaryotes detected by CARD-FISH can be attributed to one of the seven groups (six taxonomic using CARD-FISH and one by morphology when stained with DAPI) . In the epipelagic 100 m samples, only 20% of total eukaryotes fall into one of these groups. This difference is driven largely by the morphotype I call the split nucleus , which does not decrease in absolute abundance with depth, instead increasing in its proportion of the eukaryotic population in deeper waters. Lastly, I found that eukaryotic microbes, typified by two heterotrophic flagellate species which appear to be ubiquitous in the world\u27s oceans, can survive and even grow despite long-term exposure to the cold, high-pressure conditions of the deep sea, indicating that protists transported to the deep sea by advection or on particles can seed populations there

Local Structure for Vertex-Minors

This thesis is about a conjecture of Geelen on the structure of graphs with a forbidden vertex-minor; the conjecture is like the Graph Minors Structure Theorem of Robertson and Seymour but for vertex-minors instead of minors. We take a step towards proving the conjecture by determining the "local structure''. Our first main theorem is a grid theorem for vertex-minors, and our second main theorem is more like the Flat Wall Theorem of Robertson and Seymour. We believe that the results presented in this thesis provide a path towards proving the full conjecture. To make this area more accessible, we have organized the first chapter as a survey on "structure for vertex-minors''

Work ow-based systematic design of high throughput genome annotation

The genus Eimeria belongs to the phylum Apicomplexa, which includes many obligate intra-cellular protozoan parasites of man and livestock. E. tenella is one of seven species that infect the domestic chicken and cause the intestinal disease coccidiosis which is economy important for poultry industry. E. tenella is highly pathogenic and is often used as a model species for the Eimeria biology studies. In this PhD thesis, a comprehensive annotation system named as \WAGA" (Workflow-based Automatically Genome Annotation) was built and applied to the E. tenella genome. InforSense KDE, and its BioSense plug-in (products of the InforSense Company), were the core softwares used to build the workflows. Workflows were made by integrating individual bioinformatics tools into a single platform. Each workflow was designed to provide a standalone service for a particular task. Three major workflows were developed based on the genomic resources currently available for E. tenella. These were of ESTs-based gene construction, HMM-based gene prediction and protein-based annotation. Finally, a combining workflow was built to sit above the individual ones to generate a set of automatic annotations using all of the available information. The overall system and its three major components were deployed as web servers that are fully tuneable and reusable for end users. WAGA does not require users to have programming skills or knowledge of the underlying algorithms or mechanisms of its low level components. E. tenella was the target genome here and all the results obtained were displayed by GBrowse. A sample of the results is selected for experimental validation. For evaluation purpose, WAGA was also applied to another Apicomplexa parasite, Plasmodium falciparum, the causative agent of human malaria, which has been extensively annotated. The results obtained were compared with gene predictions of PHAT, a gene finder designed for and used in the P. falciparum genome project