4,765 research outputs found
Applications and Properties of Magnetic Nanoparticles
This Special Issue aimed to cover the new developments in the synthesis and characterization of magnetic nanoconstructs ranging from conventional metal oxide nanoparticles to novel molecule-based or hybrid multifunctional nano-objects. At the same time, the focus was on the potential of these novel magnetic nanoconstructs in several possible applications, e.g. sensing, energy storage, and nanomedicine
Ciguatoxins
Ciguatoxins (CTXs), which are responsible for Ciguatera fish poisoning (CFP), are liposoluble toxins produced by microalgae of the genera Gambierdiscus and Fukuyoa. This book presents 18 scientific papers that offer new information and scientific evidence on: (i) CTX occurrence in aquatic environments, with an emphasis on edible aquatic organisms; (ii) analysis methods for the determination of CTXs; (iii) advances in research on CTX-producing organisms; (iv) environmental factors involved in the presence of CTXs; and (v) the assessment of public health risks related to the presence of CTXs, as well as risk management and mitigation strategies
Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria
Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases
Extractable organics and colour in a bleached kraft mill effluent land application system and recipient ground waters
This thesis describes a study of the behaviour of extractable organics and colour in a land application system used to treat highly coloured, organic-rich, alkali extraction stage and foul condensate effluents from a traditional bleached kraft mill. The land application system comprised 44 unlined seepage basins, totalling 86 ha in area, into which approximately 10,000 m³ d⁻¹ effluent was loaded for approximately eight months of each year. The study aimed to determine (1) the effectiveness of the system for treating major effluent organics, including monoterpenes, fatty acids, resin acids, chlorophenolics, and colour, and (2) the effects of the system on organic contamination of sediments, aquifer materials, and ground waters.
The study was carried out in four parts, investigating: (i) the behaviour of extractable organics and colour in the effluent drains and seepage basins; (ii) the penetration of extractable organics into the sediments beneath the seepage basins; (iii) the organic chemistry of shallow ground waters beneath the seepage system, and of deeper off-site ground waters; and (iv) behaviour of extractable organics and colour in laboratory soil-column simulating the land application process. In addition, a review of land application of pulp mill effluents was carried out, and analytical methods for determining extractable organics in effluents, sediments, and ground waters were developed.
Concentrations of extractable organics and chlorophenolics were reduced by >95% over a 40 day period in the seepage basins. Removal rates decreased in the order fatty acids > chlorophenolics ≈ monoterpenes > resin acids. Resin acids underwent reductive and oxidative transformations, producing transient intermediates including 13-abietenoic acid and 13β-hydroxyabietanoic acid. A suite of relatively stable transformed species, dominated by the saturated compound abietanoic acid, remained in the seepage pond after 40 days. Colour removal over the same period was approximately 25%.
High concentrations of effluent-derived extractable organics were found in surficial sediments beneath the seepage basins. Major compounds were resin acids, largely saturated species, and diterpene hydrocarbon transformation products. Diterpene hydrocarbons were dominated by retene, fichtelite, and dehydroabietin. Surficial sediments contained concentrations of total resin acids and diterpene hydrocarbons of up to 10,000 mg kg⁻¹. Concentrations dropped with depth, but high levels were found in discrete zones at depths of up to 5 m beneath the surface. This indicated that effluent movement was occurring through permeable conduits rather than via uniform infiltration through the soil, and was consistent with the fractured geology of the site.
Ground waters taken from seven well clusters, sampling depths between 2 and 15 m beneath the seepage basins, contained elevated sodium and chloride concentrations (200-400 mg L⁻¹) and spatially variable colour levels (100-2000 CPU). Effluent-derived extractable organics were also found in variable concentrations. Major compounds were methyl-substituted 2-cyclopentenones, resin acids, and diterpene hydrocarbons. Resin acids and diterpene hydrocarbons were the generally dominant compound classes, concentrations totalling 20-2600 μg L⁻¹. Preliminary assessment of chlorophenolics found low levels, totalling 2-4 μg L⁻¹ in the most contaminated ground waters. The results indicated that contamination of shallow ground water was occurring, but the nature and level of this contamination was highly spatially variable. As found for the sediment studies, these findings were consistent with effluent infiltration through heterogeneous, fractured, sub-surface geology.
The hydrogeology of the area was determined to be dominated by ground water movement through fractured zones in four major ignimbrite aquifers. Wells were placed at depths between 9 and 110 m, and at distances from immediately adjacent to 2.7 km from the seepage area to sample ground water from these zones. Contamination was found largely within the highly fractured, high flow zones of two of these units, the Marshall A and, to a lesser extent, the Marshall B ignimbrite aquifers. Concentrations of effluent-sourced extractable organics (largely resin acids and diterpene hydrocarbons) and colour were highest immediately beneath the seepage area, maximum concentrations of 110 μg L⁻¹ total resin acids and diterpene hydrocarbons, and 900 CPU colour being found. Concentrations dropped rapidly with distance
from the ponds, decreasing by approximately 90% within about 100 m from the seepage area. There was evidence for retardation of organics relative to sodium and chloride in the off-site aquifers.
Laboratory simulations of effluent infiltration through seepage site soils were carried out under two application regimes (permanently flooded, and flood-dry cycle) to determine the range of treatment possibilities occurring in the seepage system. Leachate chemistry was monitored over an approximately two year period, and soil extractives measured at the end of the study. Mass balance was used to estimate effluent treatment efficiency. The flood-dry (aerobic) application regime resulted in essentially compete degradative removal of extractable organics.
Under the flooded (anaerobic) regime, extractable organic removal was limited for all constituents other than fatty acids, which were >90% removed. Resin acids were strongly retained by the soil, approximately 72% remaining in the soil at the end of the study. Approximately 25% was recovered in the leachate. Monoterpenes were highly mobile, moving rapidly through the soil. A relatively stable suite of transformed compounds was found in the leachates. Monoterpene removal was estimated to be approximately 55%. Under flooded conditions, transformation rather than degradative removal of extractable organics occurred.
Colour intensification, rather than reduction, occurred at times in both application regimes. At the end of the study, colour removal in the flood-dry cycle regime was 2%, and in the flooded regime an increase of 51% was measured.
In summary, the study found that the land application system resulted in large decreases (>95%) in the concentrations of extractable organics, but little overall treatment of effluent colour. Ground waters affected by effluent infiltration were highly variable in composition, but in general contained elevated colour levels, and moderate-to-low concentrations of extractable organics. Resin acids and diterpene hydrocarbons were the dominant class of extractable organics found in sediments and ground waters beneath the seepage system
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Prediction of Human Gut Bacterial Secreted Proteins and their Interactions with Human Colonic Proteins
The gut microbiome is known to interact with the human host and deviations from a healthy gut microbiome can have serious repercussions for host health, but our knowledge of bacterial mediators of these interactions lags behind our ability to identify correlations with the gut microbiome. In this work I utilize computational pipelines to analyze publicly available gut microbiome data to identify potential mediators of gut interactions, first between bacteria, and later with host colonic cells.
Using previously published metagenomic data from sites along the gastrointestinal tract, I charted the biogeography of bacterial secreted proteins predicted from the human gut microbiome and identify functions that are enriched along the digestive tract and in the gut mucosa and lumen. These studies provide a dataset of gut bacterial secreted proteins that can serve as a resource for studies of potential interbacterial and host-bacterial interactions, and represent the largest-scale effort to date of annotation of potential human sequence homologs in gut commensal bacteria
Evaluating Neural Networks as Cognitive Models for Learning Quasi-regularities in Language
Many aspects of language can be categorized as quasi-regular: the relationship between the inputs and outputs is systematic but allows many exceptions. Common domains that contain quasi-regularity include morphological inflection and grapheme-phoneme mapping. How humans process quasi-regularity has been debated for decades. This thesis implemented modern neural network models, transformer models, on two tasks: English past tense inflection and Chinese character naming, to investigate how transformer models perform quasi-regularity tasks. This thesis focuses on investigating to what extent the models\u27 performances can represent human behavior. The results show that the transformers\u27 performance is very similar to human behavior in many aspects, such as accuracy, answer variability, etc. However, there are still some differences in the models\u27 performance and human behavior, such as humans are more likely to produce irregular forms for nonce English verbs and are more likely to produce regular pinyin for unknown Chinese characters
Control of integrin adhesions by myotubularin and phosphatidylinositol 3-kinase C2β in a myotubular myopathy model
X-linked centronuclear myopathy (XLCNM), also known as myotubular myopathy, is a rare and severe skeletal muscle disorder that manifests with congenital hypotonia and leads to early childhood mortality due to its currently limited therapeutic options. XLCNM is caused by loss-of-function mutations in the gene encoding the lipid phosphatase myotubularin (MTM1), which dephosphorylates the phosphoinositide phosphatidylinositol 3-phosphate [PI(3)P] at endosomal membranes. Among XLCNM pathomechanisms is impaired muscle cell adhesion via integrins, the transmembrane components of focal adhesions (FAs). Integrin subunit β1 (β1-integrin) plays key roles in the formation and maintenance of specialized skeletal muscle adhesions essential to muscle function. Importantly, MTM1-mediated PI(3)P turnover plays a role in the exocytosis of integrins from endosomes to the plasma membrane, yet the impact of MTM1on cell adhesions has not been described in detail. A functional association between MTM1 and phosphatidylinositol 3-kinase C2β (PI3KC2β), a lipid kinase that synthesizes PI(3)P and phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2], was uncovered in mammals when skeletal muscle-specific ablation of PI3KC2β rescued the disease phenotype of XLCNM mouse models. Previous studies have proposed a direct rebalancing of PI(3)P levels by PI3KC2β as the mechanism underlying the rescue of XLCNM. However, the precise mechanistic interplay between MTM1 and PI3KC2β, and its relevance in skeletal muscle physiological and pathological conditions remains elusive. Thus, in this project we aimed to mechanistically characterize this functional interaction in a cell-based context relevant to XLCNM. By pursuing this objective, we intended to gain insights into the molecular pathogenesis of XLCNM and the role of PI3KC2β in this context, serving as a basis for the development of XLCNM therapeutic strategies. For this purpose, the murine myoblast cell line C2C12 was used to generate knockout (KO) cell lines lacking MTM1, PI3KC2β, or both enzymes. In this system, we described that loss of MTM1 led to cell adhesion defects evidenced by decreased cell spreading, number of FAs and surface activated β1-integrin, which functionally resulted in enhanced migration and impaired myoblast differentiation. Cell adhesion defects and correlated functional phenotypes were completely rescued by co-depletion of PI3KC2β. Contrary to the prevailing opinion, we showed that the accumulation of the MTM1 substrate PI(3)P observed in Mtm1KO myoblasts was not normalized upon co-depletion. Instead, we showed that blockage of endocytosis ameliorated adhesion defects in Mtm1KO myoblasts. Data from HeLa cells, included in this dissertation for completeness purposes, showed that PI3KC2β knockdown (KD) leads to impaired active β1 integrin internalization, a phenotype that we mechanistically explained by a role of PI3KC2β in clathrin-mediated endocytosis (CME) of active β1-integrins. Hence, we propose that MTM1 and PI3KC2β play antagonistic roles in the control of active β1-integrin adhesions by respectively mediating recycling to the plasma membrane and internalization via CME. Treatment of MTM1-depleted cells with a newly developed PI3KC2β inhibitor rescued the reported cell adhesion phenotypes, thus establishing proof-of-principle evidence for a PI3KC2β-targeted XLCNM therapy. Altogether, our findings provide insights into cell adhesion defects key to XLCNM pathogenesis in a newly established in vitro model system. Moreover, we uncover a novel function of PI3KC2β in the regulation of integrin adhesions, setting a mechanistic background for its rescue of the XLCNM disease phenotype, an essential step towards the development of therapies targeting PI3KC2β.Myotubuläre Myopathie (X-linked centrouclear myopathy; XLCNM) ist eine seltene und schwere Skelettmuskelerkrankung, die sich mit angeborener Hypotonie manifestiert und zu frühkindlicher Sterblichkeit führt aufgrund von begrenzten therapeutischen Behandlungsmöglichkeiten. XLCNM wird durch Mutation des für die Phosphatase Myotubularin (MTM1) codierenden MTM1-Gens verursacht, wodurch die zelluläre Funktion von MTM1, die Entfernung des Phosphoinositids Phosphatidylinositol-3-phosphat [PI(3)P] an endosomalen Membranen durch Dephosphorylierung, gestört wird. Einer der XLCNM Pathomechanismen ist die beeinträchtigte Muskelzell-Adhäsion mittels Integrine, die Transmembranproteine in fokalen Zelladhäsionen (FA). Die β1-Integrin-Untereinheit ist von besonderer Bedeutung in der Formation und Aufrechterhaltung von speziellen Skelettmuskel-Zelladhäsionen, welche essenziell sind für eine normale Muskelfunktion. Frühere Studien haben gezeigt, dass MTM1 durch die Konversion von PI(3)P eine Rolle bei der Exozytose von Integrinen aus Endosomen spielt. Inwiefern intrazellulärer Transport der Integrine durch MTM1 an der Bildung und Aufrechterhaltung spezialisierter Zelladhäsionen im Muskel beteiligt ist, ist jedoch unzureichend verstanden. Des Weiteren wurde eine funktionelle Assoziation zwischen MTM1 und der Phosphatidylinositol 3-Kinase C2β (PI3KC2β), einer Lipidkinase, die PI(3)P und Phosphatidylinositol-3,4-bisphosphat [PI(3,4)P2] synthetisiert, in Säugetieren beschrieben, da die skelettmuskelspezifische genetische Ausschaltung von PI3KC2β die XLCNM-assoziierten Krankheitsphänotypen in Mausmodellen revidiert. Frühere Studien haben eine Normalisierung der PI(3)P-Level durch PI3KC2β als den Mechanismus vorgeschlagen, der der Rettung von XLCNM zugrunde liegt. Allerdings ist der genaue Mechanismus, der dem inversen Zusammenhang zwischen den zellulären Funktionen von MTM1 und PI3KC2β zugrunde liegt, und dessen Relevanz in physiologischen und pathologischen Zuständen der Skelettmuskulatur, nicht vollständig erforscht. Daher war das Ziel dieser Studie, das Zusammenspiel beider Proteine in einem für XLCNM relevanten zellbasierten Kontext mechanistisch weiter aufzuklären, um so die molekulare Grundlage zur Entwicklung von therapeutischen Strategien für XLCNM durch Manipulation von PI3KC2β zu schaffen. Zu diesem Zweck wurde die murine myoblastische Zelllinie C2C12 verwendet, um Knockout (KO)-Zelllinien zu erzeugen, denen MTM1, PI3KC2β oder beide Enzyme fehlen. In diesem System konnten wir beschreiben, dass der Verlust von MTM1 zu defekter Zelladhäsion führt, da Mtm1KO Zellen eine verringerte Zellausbreitung und eine reduzierte Anzahl an FA und oberflächenaktivierten β1-Integrin zeigen, was funktionell mit einer verstärkten Migration und einer beeinträchtigten Muskelzelldifferenzierung verbunden ist. Diese Phänotypen konnten vollständig durch den Co-KO von MTM1 und PI3KC2β umgekehrt werden. Allerdings unterliegt dieser Umkehrung der XLCNM-assoziierten Phänotypen nicht die, wie in der Literatur angenommen, Akkumulation des MTM1-Substrats PI(3)P, da die durch MTM1-Verlust angereicherten PI(3)P Level durch die gleichzeitige Ausschaltung von PI3KC2β nicht reduziert werden konnten. Stattdessen zeigen wir, dass die Inhibition der Endozytose Adhäsionsdefekte in Mtm1KO-Myoblasten verbessern kann. In HeLa-Zellen resultiert der Knockdown (KD) von PI3KC2β in einer beeinträchtigten aktiven β1-Integrin Internalisierung. Mechanistisch wird dies durch eine wichtige Rolle von PI3KC2β bei der Clathrin-vermittelte Endozytose (clathrin-mediated endocytosis; CME) von aktiven β1 Integrinen erklärt. Unsere Ergebnisse unterstützen ein Modell, in dem MTM1 und PI3KC2β antagonistische Rollen bei der Kontrolle aktiver β1-Integrin-Adhäsionen zugewiesen werden, da MTM1 die Integrin Exozytose zur Plasmamembran und PI3KC2β die rückführende Internalisierung der Integrine über CME vermittelt. Weiterhin konnten wir zeigen, dass die Behandlung von Zellen, denen MTM1 fehlt, mit einem neu entwickelten PI3KC2β-Inhibitor die Zelladhäsionsphänotypen umkehren kann und liefern damit die molekulare Grundlage für eine PI3KC2β-gerichtete XLCNM-Therapie. Zusammenfassend geben unsere Ergebnisse Einblicke in Zelladhäsionsdefekte, die für die XLCNM-Pathogenese in einem neu etablierten in vitro-Modellsystem von entscheidender Bedeutung sind. Wir decken außerdem eine neue Funktion von PI3KC2β bei der Regulation von Integrin-Adhäsionen durch CME auf und schaffen einen mechanistischen Hintergrund für die Umkehrung des XLCNM-Krankheitsphänotyps durch PI3KC2β Inhibition, ein wesentlicher Schritt, der den Weg zur Entwicklung von XLCNM-Therapien ebnet
Understanding the Ecological Drivers of Virus Diversity and Evolution and the Major Transitions in RNA Virus Evolution
RNA viruses are abundant, ubiquitous, and likely infect all life forms. Due to a historical focus on species of clinical or agricultural significance, terrestrial environments have been largely overlooked from a virological perspective. We have little understanding of the roles RNA viruses play in soil biogeochemical processes or how they are influenced by their surrounding environment. In this thesis, I utilised meta-transcriptomic sequencing to generate expansive RNA sequence data from soil and sediment samples representing unique environments with the broad aim of characterising environmental viromes. I identified a total of 9,176 novel viruses from 66 families, greatly expanding the environmental virosphere. Statistical modelling of the relationship between ecological factors and virome composition revealed that viruses with plant and microbial hosts were more influenced by environmental factors than animal-infecting viruses. I also aimed to investigate the genetic and evolutionary patterns of highly divergent lineages of microbe-associated RNA viruses, such as the Picobirnaviridae and Lenarviricota. I performed phylogenetic and genomic analyses on expansive data sets of predominantly metagenomically sourced sequences, including over 2,000 sequences identified in this thesis. The highly enriched presence of bacterial gene markers and nearly zero evidence of co-evolution between picobirnaviruses and assumed hosts strongly suggest the Picobirnaviridae are a family of RNA bacteriophage. The evolutionary pathways within the Lenarviricota suggest eukaryotic RNA viruses likely arose from a levivirus-like ancestor and have undergone multiple, independent instances of capsid gene acquisition. My work suggests that viruses infecting soil-dwelling organisms are important players in global ecosystems, and provides insights into the phylogenetic relationships and genetic features of microbe-infecting RNA virus families of evolutionary and ecological significance
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