1,060 research outputs found

    Computational Analyses of Metagenomic Data

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    Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic. In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics. The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches. The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation

    Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing

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    Standalone and consortia-led single-cell atlases of healthy and diseased human airways generated with single-cell RNA-sequencing (scRNA-seq) have ushered in a new era in respiratory research. Numerous discoveries, including the pulmonary ionocyte, potentially novel cell fates, and a diversity of cell states among common and rare epithelial cell types have highlighted the extent of cellular heterogeneity and plasticity in the respiratory tract. scRNA-seq has also played a pivotal role in our understanding of host–virus interactions in coronavirus disease 2019 (COVID-19). However, as our ability to generate large quantities of scRNA-seq data increases, along with a growing number of scRNA-seq protocols and data analysis methods, new challenges related to the contextualisation and downstream applications of insights are arising. Here, we review the fundamental concept of cellular identity from the perspective of single-cell transcriptomics in the respiratory context, drawing attention to the need to generate reference annotations and to standardise the terminology used in literature. Findings about airway epithelial cell types, states and fates obtained from scRNA-seq experiments are compared and contrasted with information accumulated through the use of conventional methods. This review attempts to discuss major opportunities and to outline some of the key limitations of the modern-day scRNA-seq that need to be addressed to enable efficient and meaningful integration of scRNA-seq data from different platforms and studies, with each other as well as with data from other high-throughput sequencing-based genomic, transcriptomic and epigenetic analyses

    Modern meat: the next generation of meat from cells

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    Modern Meat is the first textbook on cultivated meat, with contributions from over 100 experts within the cultivated meat community. The Sections of Modern Meat comprise 5 broad categories of cultivated meat: Context, Impact, Science, Society, and World. The 19 chapters of Modern Meat, spread across these 5 sections, provide detailed entries on cultivated meat. They extensively tour a range of topics including the impact of cultivated meat on humans and animals, the bioprocess of cultivated meat production, how cultivated meat may become a food option in Space and on Mars, and how cultivated meat may impact the economy, culture, and tradition of Asia

    Behaviour of Listeria monocytogenes in New Zealand fresh apple supply chains

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    Listeria monocytogenes (L. monocytogenes) is a pathogenic bacterium. It can be a market access issue if found on fresh produce like apples, especially in countries with "zero tolerance" for bacteria like the USA. Although New Zealand has recorded no outbreak or recalls for apples, the potential exists for L. monocytogenes to be present on apples through the soil, water, and packhouse. The literature review found knowledge gaps in understanding the survival of L. monocytogenes under dynamic temperature conditions, which is a reality in the international or domestic supply chain. The thesis investigated: (i) The effect of dynamic temperatures on L. monocytogenes in the international supply chain, (ii) The effect of dynamic temperatures on L. monocytogenes in the domestic supply chain, (iii) The effect of storage temperatures on the survival of three lineages of L. monocytogenes on apples, (iv) The effect of commercial storage temperatures on the survival and attachment of three lineages of L. monocytogenes on two apple cultivars. In conclusion, the research has proved that dynamic temperatures in the international and domestic apple supply chains did not result in the growth of L. monocytogenes for various apple cultivars. The study also demonstrated that L. monocytogenes of lineage I and II has better survival and biofilmmaking capacity under commercially critical apple supply chain temperatures than lineages III. The comparative quantitative challenge study using MPN and qPCR methods explored options for a faster and more accurate way to quantify L. monocytogenes and found higher bacterial concentrations in the qPCR than MPN method, which could be due to nucleic acids originating from dead cells in qPCR interfering with the final results. This thesis provides helpful insights into the survival of L. monocytogenes on different apple cultivars that can be used to develop effective risk mitigation strategies for the fresh apple supply chain

    An investigation into the potential of peptide mass fingerprinting for the study of Australian faunal assemblages

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    One of the main challenges to the study of past fauna is the often high level of fragmentation of bone assemblages. Zooarchaeology by Mass Spectrometry (ZooMS) is a biomolecular method that can be used to identify fragmented bones on the basis of their unique collagen fingerprints. So far, ZooMS studies have mostly focused on Eurasian contexts, but the method also has significant potential for the study of faunal assemblages in other regions of the world. This thesis explores the potential of Zooarchaeology by Mass Spectrometry (ZooMS) to study Australian faunal assemblages. Two major challenges limiting ZooMS applications in Australia are addressed: the lack of a reference database, and limited knowledge of collagen preservation in the country. Then, the potential of ZooMS to study Australian faunal assemblages is further explored

    Northeastern Illinois University, Academic Catalog 2023-2024

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    https://neiudc.neiu.edu/catalogs/1064/thumbnail.jp

    Adaptation in the face of internal conflict:The paradox of the organism revisited

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    The paradox of the organism refers to the observation that organisms appear to function as coherent purposeful entities, despite the potential for within-organismal components like selfish genetic elements and cancer cells to erode them from within. While it is commonly accepted that organisms may pursue fitness maximisation and can be thought to hold particular agendas, there is a growing recognition that genes and cells do so as well. This can lead to evolutionary conflicts between an organism and the parts that reside within it. Here, we revisit the paradox of the organism. We first outline its conception and relationship to debates about adaptation in evolutionary biology. Second, we review the ways selfish elements may exploit organisms, and the extent to which this threatens organismal integrity. To this end, we introduce a novel classification scheme that distinguishes between selfish elements that seek to distort transmission versus those that seek to distort phenotypic traits. Our classification scheme also highlights how some selfish elements elude a multi-level selection decomposition using the Price equation. Third, we discuss how the organism can retain its status as the primary fitness-maximising agent in the face of selfish elements. The success of selfish elements is often constrained by their strategy and further limited by a combination of fitness alignment and enforcement mechanisms controlled by the organism. Finally, we argue for the need for quantitative measures of both internal conflicts and organismality

    The Self The Soul and The World: Affect Reason and Complexity

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    This book looks at the affective-cognitive roots of how the human mind inquires into the workings of nature and, more generally, how the mind confronts reality. Reality is an infinitely complex system, in virtue of which the mind can comprehend it only in bits and pieces, by making up interpretations of the myriads of signals received from the world by way of integrating those with information stored from the past. This constitutes a piecemeal interpretation by which we assemble our phenomenal reality. In perceiving the complex world and responding to it, the mind invokes the logic of affect and the logic of reason, the former mostly innate and implicit, and the latter generated consciously in explicit terms with reference to mind-independent relations between entities in nature. It is a strange combination of affect and reason that enables us to make decisions and inferences, --- the latter mostly of the inductive type --- thereby making possible the development of theories. Theories are our tool-kits for explaining and predicting phenomena, guiding us along in our journey in life. Theories, however, are defeasible, and need to be constantly updated, at times even radically. In this, the self and the soul are of enormous relevance. The former is the affect-based psychological engine driving all our mental processes, while the latter is the capacity of the conscious mind to examine and reconstruct the self by modulating repressed conflicts. If the soul remains inoperative, all our theories become misdirected and a rot spreads inexorably all around us
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