Why genes evolve faster on secondary chromosomes in bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently

Data Storage and Dissemination in Pervasive Edge Computing Environments

Nowadays, smart mobile devices generate huge amounts of data in all sorts of gatherings. Much of that data has localized and ephemeral interest, but can be of great use if shared among co-located devices. However, mobile devices often experience poor connectivity, leading to availability issues if application storage and logic are fully delegated to a remote cloud infrastructure. In turn, the edge computing paradigm pushes computations and storage beyond the data center, closer to end-user devices where data is generated and consumed. Hence, enabling the execution of certain components of edge-enabled systems directly and cooperatively on edge devices. This thesis focuses on the design and evaluation of resilient and efficient data storage and dissemination solutions for pervasive edge computing environments, operating with or without access to the network infrastructure. In line with this dichotomy, our goal can be divided into two specific scenarios. The first one is related to the absence of network infrastructure and the provision of a transient data storage and dissemination system for networks of co-located mobile devices. The second one relates with the existence of network infrastructure access and the corresponding edge computing capabilities. First, the thesis presents time-aware reactive storage (TARS), a reactive data storage and dissemination model with intrinsic time-awareness, that exploits synergies between the storage substrate and the publish/subscribe paradigm, and allows queries within a specific time scope. Next, it describes in more detail: i) Thyme, a data storage and dis- semination system for wireless edge environments, implementing TARS; ii) Parsley, a flexible and resilient group-based distributed hash table with preemptive peer relocation and a dynamic data sharding mechanism; and iii) Thyme GardenBed, a framework for data storage and dissemination across multi-region edge networks, that makes use of both device-to-device and edge interactions. The developed solutions present low overheads, while providing adequate response times for interactive usage and low energy consumption, proving to be practical in a variety of situations. They also display good load balancing and fault tolerance properties.Resumo Hoje em dia, os dispositivos móveis inteligentes geram grandes quantidades de dados em todos os tipos de aglomerações de pessoas. Muitos desses dados têm interesse loca- lizado e efêmero, mas podem ser de grande utilidade se partilhados entre dispositivos co-localizados. No entanto, os dispositivos móveis muitas vezes experienciam fraca co- nectividade, levando a problemas de disponibilidade se o armazenamento e a lógica das aplicações forem totalmente delegados numa infraestrutura remota na nuvem. Por sua vez, o paradigma de computação na periferia da rede leva as computações e o armazena- mento para além dos centros de dados, para mais perto dos dispositivos dos utilizadores finais onde os dados são gerados e consumidos. Assim, permitindo a execução de certos componentes de sistemas direta e cooperativamente em dispositivos na periferia da rede. Esta tese foca-se no desenho e avaliação de soluções resilientes e eficientes para arma- zenamento e disseminação de dados em ambientes pervasivos de computação na periferia da rede, operando com ou sem acesso à infraestrutura de rede. Em linha com esta dico- tomia, o nosso objetivo pode ser dividido em dois cenários específicos. O primeiro está relacionado com a ausência de infraestrutura de rede e o fornecimento de um sistema efêmero de armazenamento e disseminação de dados para redes de dispositivos móveis co-localizados. O segundo diz respeito à existência de acesso à infraestrutura de rede e aos recursos de computação na periferia da rede correspondentes. Primeiramente, a tese apresenta armazenamento reativo ciente do tempo (ARCT), um modelo reativo de armazenamento e disseminação de dados com percepção intrínseca do tempo, que explora sinergias entre o substrato de armazenamento e o paradigma pu- blicação/subscrição, e permite consultas num escopo de tempo específico. De seguida, descreve em mais detalhe: i) Thyme, um sistema de armazenamento e disseminação de dados para ambientes sem fios na periferia da rede, que implementa ARCT; ii) Pars- ley, uma tabela de dispersão distribuída flexível e resiliente baseada em grupos, com realocação preventiva de nós e um mecanismo de particionamento dinâmico de dados; e iii) Thyme GardenBed, um sistema para armazenamento e disseminação de dados em redes multi-regionais na periferia da rede, que faz uso de interações entre dispositivos e com a periferia da rede. As soluções desenvolvidas apresentam baixos custos, proporcionando tempos de res- posta adequados para uso interativo e baixo consumo de energia, demonstrando serem práticas nas mais diversas situações. Estas soluções também exibem boas propriedades de balanceamento de carga e tolerância a faltas

The mitochondrial genome of Sinentomon erythranum (Arthropoda: Hexapoda: Protura): an example of highly divergent evolution

<p>Abstract</p> <p>Background</p> <p>The phylogenetic position of the Protura, traditionally considered the most basal hexapod group, is disputed because it has many unique morphological characters compared with other hexapods. Although mitochondrial genome information has been used extensively in phylogenetic studies, such information is not available for the Protura. This has impeded phylogenetic studies on this taxon, as well as the evolution of the arthropod mitochondrial genome.</p> <p>Results</p> <p>In this study, the mitochondrial genome of <it>Sinentomon erythranum </it>was sequenced, as the first proturan species to be reported. The genome contains a number of special features that differ from those of other hexapods and arthropods. As a very small arthropod mitochondrial genome, its 14,491 nucleotides encode 37 typical mitochondrial genes. Compared with other metazoan mtDNA, it has the most biased nucleotide composition with T = 52.4%, an extreme and reversed AT-skew of -0.351 and a GC-skew of 0.350. Two tandemly repeated regions occur in the A+T-rich region, and both could form stable stem-loop structures. Eighteen of the 22 tRNAs are greatly reduced in size with truncated secondary structures. The gene order is novel among available arthropod mitochondrial genomes. Rearrangements have involved in not only small tRNA genes, but also PCGs (protein-coding genes) and ribosome RNA genes. A large block of genes has experienced inversion and another nearby block has been reshuffled, which can be explained by the tandem duplication and random loss model. The most remarkable finding is that <it>trnL2(UUR) </it>is not located between <it>cox1 </it>and <it>cox2 </it>as observed in most hexapod and crustacean groups, but is between <it>rrnL </it>and <it>nad1 </it>as in the ancestral arthropod ground pattern. The "<it>cox1</it>-<it>cox2</it>" pattern was further confirmed in three more representative proturan species. The phylogenetic analyses based on the amino acid sequences of 13 mitochondrial PCGs suggest <it>S</it>. <it>erythranum </it>failed to group with other hexapod groups.</p> <p>Conclusions</p> <p>The mitochondrial genome of <it>S. erythranum </it>shows many different features from other hexapod and arthropod mitochondrial genomes. It underwent highly divergent evolution. The "<it>cox1</it>-<it>cox2</it>" pattern probably represents the ancestral state for all proturan mitogenomes, and suggests a long evolutionary history for the Protura.</p

Structuring visual exploratory analysis of skill demand

The analysis of increasingly large and diverse data for meaningful interpretation and question answering is handicapped by human cognitive limitations. Consequently, semi-automatic abstraction of complex data within structured information spaces becomes increasingly important, if its knowledge content is to support intuitive, exploratory discovery. Exploration of skill demand is an area where regularly updated, multi-dimensional data may be exploited to assess capability within the workforce to manage the demands of the modern, technology- and data-driven economy. The knowledge derived may be employed by skilled practitioners in defining career pathways, to identify where, when and how to update their skillsets in line with advancing technology and changing work demands. This same knowledge may also be used to identify the combination of skills essential in recruiting for new roles. To address the challenges inherent in exploring the complex, heterogeneous, dynamic data that feeds into such applications, we investigate the use of an ontology to guide structuring of the information space, to allow individuals and institutions to interactively explore and interpret the dynamic skill demand landscape for their specific needs. As a test case we consider the relatively new and highly dynamic field of Data Science, where insightful, exploratory data analysis and knowledge discovery are critical. We employ context-driven and task-centred scenarios to explore our research questions and guide iterative design, development and formative evaluation of our ontology-driven, visual exploratory discovery and analysis approach, to measure where it adds value to users’ analytical activity. Our findings reinforce the potential in our approach, and point us to future paths to build on

Automatic processing of induced seismicity at the geothermal reservoirs Landau and Insheim

Besides political and striking uncertainty, induced seismicity is a fundamental risk to the success of geothermal projects. The geothermal reservoirs Landau and Insheim are located on the western rim of the Upper Rhine Graben where the highest fluid temperatures in Germany provide a good foundation for geothermal energy production while the complex tectonic structure provides a difficult set-up for geophysical investigations. In this thesis I advance automatic processing algorithms and apply them to assess characteristics of induced seismicity at the two geothermal reservoirs. Key objectives are to complete existing detection catalogs, determine the reliability of automatic processing results and to identify characteristics of induced earthquakes at the geothermal reservoirs which in future may be linked to operational parameters of the power plants. Challenging the completeness of existing catalogs a complementary offline similarity detection approach which considers multiple master events per reservoir is proposed. The second algorithm is an autoregressive prediction (AR)-Akaike Information Criterion (AIC)-cost-function arrival time determination approach which is straightforward trainable for different datasets on different scales and able to reliably pick robust seismic P- and S-phase arrival times on single- and multi-component data. The resulting hypocenter offsets standard deviations are approximately 1 km horizontally as well as vertically. Finally from hypocenter relative relocations, I am able to identify a spatial separation of the Insheim earthquake clusters retrieved by the similarity detection algorithm. Two orientations of seismicity are found to coincide with the stress regimes, firstly a south-east to north-west orientation during graben activity, and secondly a rather south-to-north orientation of the recently more dominant stress regime from Alpine denudation

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently