Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

Abstract The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

Abstract We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both \u3b1- and \u3b2-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the \u3b2-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis

Geothermal heat flux is the dominant source of uncertainty in englacial-temperature-based dating of ice rise formation

Ice rises are areas of locally grounded, slow-moving ice adjacent to floating ice shelves. Temperature profiles measured through ice rises contain information regarding changes to their dynamic evolution and external forcings, such as past surface temperatures, past accumulation rates and geothermal heat flux. While previous work has used borehole temperature–depth measurements to infer one or two such parameters, there has been no systematic investigation of parameter sensitivity to the interplay of multiple external forcings and dynamic changes. A one-dimensional vertical heat flow forward model developed here examines how changing forcings affect temperature profiles. Further, using both synthetic data and previous measurements from the Crary Ice Rise in Antarctica, we use our model in a Markov chain Monte Carlo inversion to demonstrate that this method has potential as a useful dating technique that can be implemented at ice rises across Antarctica. However, we also highlight the non-uniqueness of previous ice rise formation dating based on temperature profiles, showing that using nominal values for forcing parameters, without taking into account their realistic uncertainties, can lead to underestimation of dating uncertainty. In particular, geothermal heat flux represents the dominant source of uncertainty in ice rise age estimation. For instance, in Crary Ice Rise higher heat flux values (i.e. about 90 mW m−2) yield grounding timing of 1400 ± 800 years, whereas lower heat flux of around 60 mW m−2 implies earlier ice rise formation and lower uncertainties in the ice rise age estimations (500 ± 250 years). We discuss the utility of this method in choosing future ice drilling sites and conclude that integrating this technique with other indirect dating methods can provide useful constraints on past forcings and changing boundary conditions from in situ temperature–depth measurements.</p

Tomographic errors from wavefront healing: more than just a fast bias

Wave front healing, in which diffractions interfere with directly travelling waves causing a reduction in recorded traveltime delays, has been postulated to cause a bias towards faster estimated earth models. This paper reviews the theory from the mathematical physics community that explains the properties of diffractions and applies it to a suite of increasingly complicated numerical examples. We focus in particular on the elastic case and on the differences between P and S healing. We find that rather than introducing a systemic fast bias, wave front healing gives a more complicated bias in the results of traveltime tomography, with fast anomalies even manifesting themselves as slow anomalies in some situations. Of particular interest, we find that a negative correlation between the bulk and shear or compressional velocities may result to a large extend from healing.Netherlands Organization for Scientific Research (NWO:VICI865.03.007

PODER MACIO – Um processo de tradução do poema coreano Chiclete a partir de uma perspectiva das Artes Visuais

O presente texto ensaístico é um escrito de artista que aborda, em estilo de fluxo de consciência, diversas questões disparadas pelo processo de tradução do poema “Chiclete”, do poeta coreano Kim Ki-taek, durante o isolamento social provocado pela pandemia de Covid-19, em 2020 e 2021. A prática de tradução, aqui, é pensada como transformação e ampliação de sentidos, indo além da questão da equivalência de palavras. Com isso, busca-se enfatizar as ressonâncias e os desdobramentos da tradução em outras formas de arte, como performance, vídeo, escultura digital e documentação

Enquadramento performativo como trabalho de arte no Pivô Satélite #3

The article proposes the notion of performative enframing to denominate inscription practices that produce more or less normative identification effects. To demonstrate the presence and relevance of this notion in contemporary art, we analyzed two recent brazilian artworks, by Laura Fraiz and Eduardo Montelli, which were developed in the curatorial project of Raphael Fonseca for the third edition of “Pivô Satélite”, entitled “Sex, Lies, and Videotape”.O artigo propõe a noção de enquadramento performativo para nomear práticas de inscrição que produzem efeitos mais ou menos normativos de identificação de sujeitos sociais. Para demonstrar a presença e a relevância dessa noção na arte da atualidade, analisamos duas obras brasileiras recentes, de Laura Fraiz e de Eduardo Montelli, que foram desenvolvidas no projeto curatorial de Raphael Fonseca para a terceira edição do Pivô Satélite, intitulado “Sexo, Mentiras e Videotape”

Aplicação da espectroscopia no infravermelho próximo para predição da viscosidade na etapa de deslignificação do processo produtivo de celulose

Na busca por opções mais eficientes e confiáveis para caracterizar de maneira rápida e simples as propriedades da polpa celulósica, destaca-se o uso de técnicas não destrutivas, como a espectroscopia no infravermelho próximo (NIRS). O objetivo deste estudo foi aplicar a técnica NIRS para prever a viscosidade da polpa celulósica resultante da etapa inicial de deslignificação, que é parte do processo de branqueamento na produção de celulose. A intenção era avaliar a possibilidade de substituir o método de referência (NBR ISO 5351) pelo uso da técnica NIRS. Foram medidas as viscosidades de 132 amostras, das quais 104 foram utilizadas para construir um modelo de calibração multivariável (utilizando o método de mínimos quadrados parciais - PLS) e para realizar a validação cruzada, enquanto as 28 amostras restantes foram usadas para a validação externa. O equipamento NIR da marca Metrohm, modelo DS2500, foi utilizado para fazer as leituras na faixa de comprimento de onda entre 1000 e 2477,50 nm. O software escolhido para construir os modelos matemáticos foi o The Unscrambler, versão 10. Embora o algoritmo Jackknife tenha sido empregado para aprimorar os modelos, os resultados obtidos ainda apresentaram desempenho insatisfatório. Na validação externa, a previsão da viscosidade apresentou um erro médio relativo de 3% e um erro médio absoluto de 28 dm3/kg, em comparação com os resultados obtidos pelo método de referência.In the search for new options for rapid, simple, and reliable characterization of cellulose pulp properties, non-destructive techniques stand out, such as Near-Infrared Spectroscopy (NIRS). The aim of this study was to apply the NIRS technique to predict the viscosity of cellulose pulp from delignification, the initial stage of bleaching in the cellulose production process, in order to assess the feasibility of replacing the reference method (NBR ISO 5351) with the NIRS technique. The viscosity of 132 samples was determined, with 104 being used for the construction of the multivariate calibration model (Partial Least Squares - PLS method) and cross-validation, and 28 samples used for external validation. The NIR equipment used was the Metrohm brand, model DS2500, and the software used for the construction of the mathematical models was The Unscrambler, version 10. Readings were taken in the range of 1000 to 2477.50 nm. The Jackknife algorithm was employed to improve the models, but they showed low performances. External validation resulted in a relative mean error of 3% and an absolute mean error of 28 dm3/kg in the viscosity prediction when compared to results obtained from the reference method

Studio e Sperimentazione di Tecnologie di Machine Learning in Ambito Genomico ed Healthcare

Le applicazioni di intelligenza artificiale stanno rivoluzionando la nostra società, rendendo quasi ordinari compiti che fino a qualche anno fa erano considerati inaffrontabili. Casi di successo eclatanti sono all'ordine del giorno nei più disparati settori disciplinari che vanno dall'astronomia, ai sistemi produttivi e logistici, all'arte, fino alla medicina. In particolare in ambito healthcare, negli ultimi anni, si stanno moltiplicando gli studi riguardanti il microbiota (o microbioma) intestinale, un aggregato di microorganismi dal peso complessivo di circa 2Kg che vivono in simbiosi con il tratto intestinale. Altri settori in cui applicazioni intelligenti sono utilizzate con sempre maggior successo, comprendono anche la genomica, un settore dove uno dei problemi è la grandissima quantità di dati da gestire, rappresentare ed elaborare. Lo scopo di questa tesi è applicare a due casi di studio diversi algoritmi di machine learning e produrre confronti tra vari modelli evidenziando come i metodi ensemble ottengono risultati in alcuni casi migliori dei lavori in letteratura. I casi di studio presi in esame riguardano sia lo sviluppo di esperimenti per la scoperta di annotazioni Gene Ontology, ossia di nuove funzione biologiche di geni, sia di esperimenti riguardanti l'associazione tra composizione batterica del microbiota ed alcune gravi patologie, come cancro colon-rettale, morbo di Chron, morbo di Parkinson, disturbi dello spettro autistico ed artrite reumatoide