72 research outputs found

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Endogenous UMIs as quantifiable reporter elements – validation studies & applications in rAAV vectorology

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    In the creation of recombinant adeno-associated viral (rAAV) vectors, terminal DNA elements known ITRs (inverted terminal repeats) of the direct the intracellular synthesis and packaging of nonviral DNA. The need to clonally amplify ITR sequences in one form or another thereby underlies the existence of all rAAV clinical products and research materials worldwide. Their tendency to form strong nonduplex structures raises problems. The genetic precursors to rAAV vectors – typically prokaryotic plasmids – are known to possess heterogenous ITR sequences as a result of replicational instability, the effects of which on vector yield and efficacy are unclear and have not been systematically explored. To shed much-needed light on this decades-old problem, I utilised unique molecular identifiers (UMIs) as reporter elements for different rAAV plasmid preparations, so that massively parallel sequencing could be used to analyse their DNA and RNA derivatives through the course of production and in vivo gene transfer. The range of vector potencies observed, while not calamitous, definitively erases the notion that this problem can be further overlooked. The success of this unconventional strategy proved to be an equally notable outcome, offering unprecedented insights into population kinetics, and achieving quantitative consistency between biological replicates comparable to q/dPCR measurement replicates of single samples. This triggered concerted efforts to formally investigate the capabilities of UMIs used in this fashion. The probabilistic principles underlying the technique were formalised and empirically validated, confirming precision capabilities akin if not superior to dPCR and qPCR at equivalent levels of stringency. Experiments also revealed a pattern of measurement bias with potentially adverse implications for other areas of count analysis including differential gene expression

    LIPIcs, Volume 244, ESA 2022, Complete Volume

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    LIPIcs, Volume 244, ESA 2022, Complete Volum

    Light On String Solving: Approaches to Efficiently and Correctly Solving String Constraints

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    Widespread use of string solvers in formal analysis of string-heavy programs has led to a growing demand for more efficient and reliable techniques which can be applied in this context, especially for real-world cases. Designing an algorithm for the (generally undecidable) satisfiability problem for systems of string constraints requires a thorough understanding of the structure of constraints present in the targeted cases. We target the aforementioned case in different perspectives: We present an algorithm which works by reformulating the satisfiability of bounded word equations as a reachability problem for non-deterministic finite automata. Secondly, we present a transformation-system-based technique to solving string constraints. Thirdly, we investigate benchmarks presented in the literature containing regular expression membership predicates and design a decission procedure for a PSPACE-complete sub-theory. Additionally, we introduce a new benchmarking framework for string solvers and use it to showcase the power of our algorithms via an extensive empirical evaluation over a diverse set of benchmarks

    Phototrophic Bacteria

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    Microorganisms is pleased to publish this book, which reprints papers that appeared in a Special Issue on “Phototrophic Bacteria”, with Guest Editors Robert Blankenship and Matthew Sattley. This Special Issue included research on all types of phototrophic bacteria, including both anoxygenic and oxygenic forms. Research on these bacterial organisms has greatly advanced our understanding of the basic principles that underlie the energy storage that takes place in all types of photosynthetic organisms, including both bacterial and eukaryotic forms. Topics of interest include: microbial physiology, microbial ecology, microbial genetics, evolutionary microbiology, systems microbiology, agricultural microbiology, microbial biotechnology, and environmental microbiology, as all are related to phototrophic bacteria

    Noncommutative lattices

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    The extended study of non-commutative lattices was begun in 1949 by Ernst Pascual Jordan, a theoretical and mathematical physicist and co-worker of Max Born and Werner Karl Heisenberg. Jordan introduced noncommutative lattices as algebraic structures potentially suitable to encompass the logic of the quantum world. The modern theory of noncommutative lattices began 40 years later with Jonathan Leech\u27s 1989 paper "Skew lattices in rings." Recently, noncommutative generalizations of lattices and related structures have seen an upsurge in interest, with new ideas and applications emerging, from quasilattices to skew Heyting algebras. Much of this activity is derived in some way from the initiation, over thirty years ago, of Jonathan Leech\u27s program of research that studied noncommutative variations of lattices. The present book consists of seven chapters, mainly covering skew lattices, quasilattices and paralattices, skew lattices of idempotents in rings and skew Boolean algebras. As such, it is the first research monograph covering major results due to the renewed study of noncommutative lattices. It will serve as a valuable graduate textbook on the subject, as well as handy reference to researchers of noncommutative algebras

    Current Frontiers and Perspectives in Cell Biology

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    A numerous internationally renowned authors in the pages of this book present the views of the fields of cell biology and their own research results or review of current knowledge. Chapters are divided into five sections that are dedicated to cell structures and functions, genetic material, regulatory mechanisms, cellular biomedicine and new methods in cell biology. Multidisciplinary and often quite versatile approach by many authors have imposed restrictions of this classification, so it is certain that many chapters could belong to the other sections of this book. The current frontiers, on the manner in which they described in the book, can be a good inspiration to many readers for further improving, and perspectives which are highlighted can be seen in many areas of fundamental biology, biomedicine, biotechnology and other applications of knowledge of cell biology. The book will be very useful for beginners to gain insight into new area, as well as experts to find new facts and expanding horizons

    An investigation of the role of Arabidopsis thaliana plant natriuretic peptide in planta

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    The sessile nature of plants demands that they respond appropriately to changes in their environment (stresses) in order to survive. Critical to survival is the maintenance of water and ion homeostasis. The mechanisms by which plants achieve this are poorly understood. Traditionally plant stress responses were thought to be communicated by five classical plant hormones - auxin, cytokine, gibberellic acid, absisic acid and ethylene. Nowadays a plethora of other molecules are known to fulfil this function including nitric oxide, salicylic acid, jasmonic acid, brassinosteroids and peptide hormones. Plant natriuretic peptides have been proposed to be peptide hormones involved in maintaining water and ion homeostasis in plants. Evidence for this has been provided by studies of plant responses to exogenous natriuretic peptide treatment, however a demonstration of their function in planta remains outstanding. This study was undertaken to gain insight into the mechanisms regulating water and ion homeostasis in Arabdopsis by examining second messenger responses to stresses that perturb water and ion homeostasis; characterization of an Arabidopsis thaliana plant natriuretic peptide (atpnp-a) mutant and transcriptome analysis of AtPNP-A, in order to establish whether AtPNP-A plays a role in maintaining water and ion homeostasis in planta. Results indicated that recombinant AtPNP-A induces second messenger responses reminiscent of the response to NaCl, suggesting that AtPNP-A may play a signalling role in response to disturbances in water and ion homeostasis. In support of this, characterization of an atpnp-a mutant revealed that AtPNP-A is likely to be involved in processes that require adjustments to water and ion homeostasis including cell expansion, stomatal opening and NaCl and osmotic stress responses, consistent with reported responses to natriuretic peptide treatment. Furthermore, the atpnp-a mutant revealed a role for AtPNP-A in the defence response. Evidence to support this came from the computational analysis of AtPNP-A expression which correlates with genes involved in the defence response. Additionally, the transcriptome response to recombinant AtPNP-A treatment further implicated the involvement of AtPNP-A in the defence response. Therefore AtPNP-A is hypothesized to play a role in growth, abiotic and biotic stress responses that enables the plant to mount an integrated response to the environment

    Modelos de compressão e ferramentas para dados ómicos

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    The ever-increasing growth of the development of high-throughput sequencing technologies and as a consequence, generation of a huge volume of data, has revolutionized biological research and discovery. Motivated by that, we investigate in this thesis the methods which are capable of providing an efficient representation of omics data in compressed or encrypted manner, and then, we employ them to analyze omics data. First and foremost, we describe a number of measures for the purpose of quantifying information in and between omics sequences. Then, we present finite-context models (FCMs), substitution-tolerant Markov models (STMMs) and a combination of the two, which are specialized in modeling biological data, in order for data compression and analysis. To ease the storage of the aforementioned data deluge, we design two lossless data compressors for genomic and one for proteomic data. The methods work on the basis of (a) a combination of FCMs and STMMs or (b) the mentioned combination along with repeat models and a competitive prediction model. Tested on various synthetic and real data showed their outperformance over the previously proposed methods in terms of compression ratio. Privacy of genomic data is a topic that has been recently focused by developments in the field of personalized medicine. We propose a tool that is able to represent genomic data in a securely encrypted fashion, and at the same time, is able to compact FASTA and FASTQ sequences by a factor of three. It employs AES encryption accompanied by a shuffling mechanism for improving the data security. The results show it is faster than general-purpose and special-purpose algorithms. Compression techniques can be employed for analysis of omics data. Having this in mind, we investigate the identification of unique regions in a species with respect to close species, that can give us an insight into evolutionary traits. For this purpose, we design two alignment-free tools that can accurately find and visualize distinct regions among two collections of DNA or protein sequences. Tested on modern humans with respect to Neanderthals, we found a number of absent regions in Neanderthals that may express new functionalities associated with evolution of modern humans. Finally, we investigate the identification of genomic rearrangements, that have important roles in genetic disorders and cancer, by employing a compression technique. For this purpose, we design a tool that is able to accurately localize and visualize small- and large-scale rearrangements between two genomic sequences. The results of applying the proposed tool on several synthetic and real data conformed to the results partially reported by wet laboratory approaches, e.g., FISH analysis.O crescente crescimento do desenvolvimento de tecnologias de sequenciamento de alto rendimento e, como consequência, a geração de um enorme volume de dados, revolucionou a pesquisa e descoberta biológica. Motivados por isso, nesta tese investigamos os métodos que fornecem uma representação eficiente de dados ómicros de maneira compactada ou criptografada e, posteriormente, os usamos para análise. Em primeiro lugar, descrevemos uma série de medidas com o objetivo de quantificar informação em e entre sequencias ómicas. Em seguida, apresentamos modelos de contexto finito (FCMs), modelos de Markov tolerantes a substituição (STMMs) e uma combinação dos dois, especializados na modelagem de dados biológicos, para compactação e análise de dados. Para facilitar o armazenamento do dilúvio de dados acima mencionado, desenvolvemos dois compressores de dados sem perda para dados genómicos e um para dados proteómicos. Os métodos funcionam com base em (a) uma combinação de FCMs e STMMs ou (b) na combinação mencionada, juntamente com modelos de repetição e um modelo de previsão competitiva. Testados em vários dados sintéticos e reais mostraram a sua eficiência sobre os métodos do estado-de-arte em termos de taxa de compressão. A privacidade dos dados genómicos é um tópico recentemente focado nos desenvolvimentos do campo da medicina personalizada. Propomos uma ferramenta capaz de representar dados genómicos de maneira criptografada com segurança e, ao mesmo tempo, compactando as sequencias FASTA e FASTQ para um fator de três. Emprega criptografia AES acompanhada de um mecanismo de embaralhamento para melhorar a segurança dos dados. Os resultados mostram que ´e mais rápido que os algoritmos de uso geral e específico. As técnicas de compressão podem ser exploradas para análise de dados ómicos. Tendo isso em mente, investigamos a identificação de regiões únicas em uma espécie em relação a espécies próximas, que nos podem dar uma visão das características evolutivas. Para esse fim, desenvolvemos duas ferramentas livres de alinhamento que podem encontrar e visualizar com precisão regiões distintas entre duas coleções de sequências de DNA ou proteínas. Testados em humanos modernos em relação a neandertais, encontrámos várias regiões ausentes nos neandertais que podem expressar novas funcionalidades associadas à evolução dos humanos modernos. Por último, investigamos a identificação de rearranjos genómicos, que têm papéis importantes em desordens genéticas e cancro, empregando uma técnica de compressão. Para esse fim, desenvolvemos uma ferramenta capaz de localizar e visualizar com precisão os rearranjos em pequena e grande escala entre duas sequências genómicas. Os resultados da aplicação da ferramenta proposta, em vários dados sintéticos e reais, estão em conformidade com os resultados parcialmente relatados por abordagens laboratoriais, por exemplo, análise FISH.Programa Doutoral em Engenharia Informátic
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