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Improvements in natural product biosynthetic gene clusters research and functional trait-based approaches in metagenomics
No full textMicroorganisms encompass a vast metabolic and genetic diversity and are key drivers of ecosystem functioning. Metagenomics, by allowing access to the genomic material obtained directly from the environment, represents a major field of research in microbiology. The recent advent of high-throughput sequencing technologies has pushed the scale and scope of metagenomic studies. Today more than ever, metagenomics is critical to advance our knowledge of microorganisms. The research work presented in this thesis develops two (interconnected) lines of research in the field of metagenomics. The first of these is the study of natural product Biosynthetic Gene Clusters (BGCs). Microorganisms encode a large diversity of BGCs responsible for the production of several compounds with valuable industrial applications. BGCs are also important from an ecological perspective, as these participate in interactions between organisms and with the environment. To improve the exploitation of metagenomic data in BGC exploration analyses, we developed the Biosynthetic Gene Cluster Metagenomic Exploration toolbox (BiG-MEx). BiG-MEx is able to rapidly estimate the BGC domain and chemical class composition of a metagenomic sample, and perform a series of domain diversity analyses. The second research line developed in this thesis is the application of functional trait-based approaches in metagenomics. Functional traits provide valuable information to study different aspects of microorganisms’ ecology. We developed a series of tools to quantify different metagenomic functional traits, including the average genome size, 16S rRNA gene average copy number, functional diversity, and percentage of transcription factors, among others. In conclusion, this thesis contributes to the advancement of BGC mining analyses and the application of functional trait-based approaches in metagenomics
Trait-based modeling of coral-algae symbiosis in a warming ocean
No full textCoral polyps of the order Scleractinia are tiny anemone-like invertebrates interconnected through a common gastrovascular system. Scleractinian corals accrete a carbonate exoskeleton and act as primary builders of limestone structures called coral reefs in the shallow, well-lit and nutrient-poor waters of the tropics. A myriad of other organisms benefits from reef structures, making coral reefs one of the most diverse and productive ecosystems on Earth. The most puzzling aspect about corals is that they thrive in nutrient-poor waters of the tropics. The reason is inherent to a symbiotic association that they form with unicellular photoautotrophs known as zooxanthellae, located in membrane-bound vacuoles, the symbiosomes, in the corals' endodermal cells. Corals host millions of zooxanthellae algae and benefit from the carbohydrates produced from algal photosynthesis. As a result, corals do not rely exclusively on external nutrient sources. Increasing sea surface temperature induces a breakdown of the coral-algae association, causing the whitening of the corals due to a loss of zooxanthellae cells or zooxanthellae pigments, a process called bleaching. Consequently, in a warming world, the future of corals and the rich ecosystem they contribute to create is a matter of great concern. The work presented in this thesis investigates the acclimation capacity of corals under global warming and proposes potential mechanisms for explaining symbiont shuffling. These new model theories can be tested with laboratory experiments thus contributing to the development of strategies for the preservation and restoration of coral reef ecosystems
To Understand Transport Dynamics of Outer Membrane Bacterial protein Channels
No full textThe outer membrane of Gram-negative bacteria is associated with a channel called porins, designed to facilitate the transport (uptake) of nutrients and small molecules. In biological channels, the flux is very low (typically 1-1,000 s-1), and it is challenging to detect such small quantity through a direct and straightforward approach. To characterise the uptake, a general and simple method is required to quantify such molecules. To access direct information on the flux of nutrient and small molecules, we try to exploit electrophysiology as a method.
In this thesis, we use electrophysiology (single molecule electrical detection) as a tool to understand the transport and flux through outer membrane channels. Before approaching the problem of flux quantification, one needs to address a few open questions like: What is the difference between a real translocation and binding? Can we detect small molecules (size < 300 Da)? How can we improvise the detection process? etc. . In electrophysiology, we often observe fluctuation in time series of ion current signal in the presence of a molecule of interest, and thus specific conclusion on the transport properties (event rate and residence time) can be drawn, but it is often difficult to conclude on the real translocations. Next, we probe the forces involved in the translocation of such molecules. Based on the channel preference (selectivity) under the application of biased transmembrane potential, it induces a transverse fluid flow (Electroosmotic flow (EOF)) inside a channel, which drives these molecules through them by either enhancing the effect on the detection (translocation) or by hindering their pathway. Overall, the research carried out in this thesis contributes to the understanding of the electrophysiology-based study of flux quantification and the dynamics of molecular through Outer membrane channel of Gram-negative bacteria in the artificial membrane and native membrane system
Drug-related Violence in Brazil: Narratives in Brazilian TV Annual Reviews (2000 to 2015)
No full textMy computer-aided analysis of the ‘War on Drugs’ in the Brazilian TV Annual News Reviews by the Rede Globo network (Retrospectivas), from 2000 to 2015, uncovers major patterns in these particular media narratives. My mixed-methods research design combines a quantitative content analysis of the most pertinent 16 episodes of Rede Globo’s Annual Reviews with the qualitative content analysis that scrutinizes the 24 segments and the 306 stories on drug-related violence. Combining historical studies, cultural theories, media studies, concepts from international criminology, official laws, and semi-official documents highlights long-term extreme socioeconomic inequalities, race hate, social stigmatization, structural violence, lethal victimization of nonwhite males, drug illegalization, and anti-drug legislation that effectively condition contemporary drug-related violence. Various reports of the United Nations Office on Drugs and Crime and several other international and national organizations were analyzed to discuss the more recent illegalization of natural and synthetic substances and the illicit use of prescription medicaments. Brazil became an important player in the “Andean narcotic route” and turned out to be the world’s largest consumer of crack and the second largest user of cocaine after the USA. The illegalization of substances, anti-drug policies, the banalization of arbitrary violence and the lack of respect for human rights have fomented the emergence of powerful and well-structured comandos armados and violent paramilitary groups, like death squads and militias, since the beginning of the 1970s. Moreover, the ‘War on Drugs’ strategy implanted in Brazil in the 1960s, with a major focus on militarized repression rather than prevention has contributed to the increasing incidence of vulnerable drug addicts, brutal violence, homicides, disproportionate drug enforcement sentencing practices and the skyrocketing rates of incarceration of black and mestizo
Comparison of chlorogenic acid and lipid profiles in green and roasted coffee beans
No full textCoffee production and consumption continuously increase despite the numerous barriers to its cultivation and global trade. The unique, refreshing and stimulating satisfactions associated with final coffee cup quality are among the reasons for the growing production and consumption rates. Coffee quality is a multidimensional feature, certainly influenced by the origin, plant variety, different forms of cultivation and post-harvest processing. Apparently, over 60% of the elements of coffee quality are determined by postharvest processing, which involves storage and roasting. This study aims to investigate the effects of long-term storage on some of the essential chemical constituents of the green and roasted coffee bean, and most importantly on the two main coffee varieties Coffea arabica and Coffea canephora.
Moreover, various dynamics such as environmental factors, duration of storage, coffee bean varieties and market conditions largely influence the optimal storage conditions. The viability and quality of preserving coffee beans in their active physiological system are highly affected by the different storage conditions. Environmental factors such as moisture, temperature, relative humidity and different air compositions (gases) are among the core dynamic forces of storage conditions.
The thesis investigation is sub-divided into seven chapters. Chapter 1 covers the introductory part, which encompasses the history and evolution of coffee, botanical classification and cultivation, economic importance, classes of compounds present in coffee, occurrence, dietary burden, biosynthesis and biological activities; and the aim of the project. Chapter 2 composes of profiling, identification and quantification of chlorogenic acids (CGAs) in green coffee; including the use of CGAs as a resourceful tool to discriminate between Coffea arabica and Coffea canephora by employing the use of nuclear magnetic resonance and tandem mass spectrometry (MS/MS) for accurate profiling..
Synthesis of Peroxo-Cerium- and Zirconium-Containing Polyoxometalates and Homogeneous Oxidation Catalysis Studies
No full textPolyoxometalates (POMs) are discrete, anionic metal-oxo clusters which draw much attention due to their fascinating structural and compositional diversity combined with manifold properties in the areas of catalysis, magnetism, material science and medicine. The main focus of this thesis is on the incorporation of lanthanide-peroxo fragments in POMs, as such materials (i) are of interest for redox catalysis and (ii) have never been explored systematically.
This thesis comprises six chapters: Chapter 1 provides an introduction of POM chemistry as well as peroxo-containing coordination complexes of d- and f-block metals. Chapter 2 contains (i) the synthetic procedures of various lacunary POM precursors and (ii) a brief description of the instrumental techniques used for the characterization of the novel compounds reported here. Chapter 3 reports the synthesis and structural characterization of the first examples of cerium(IV)-peroxo POMs such as the trimeric 6-cerium(IV)-9-peroxo-30-tungsto-3-germanate [CeIV6(O2)9(α-GeW10O37)3]24- (1). Polyanion 1 was characterized in the solid state by single-crystal X-ray diffraction, FT-IR spectroscopy, thermogravimetric analysis, and X-ray photoelectron spectroscopy, and in solution by 183W NMR and Raman spectroscopy, as well as theoretical DFT calculations. Both POMs were shown to act as selective homogeneous catalysts for the oxidation of methionine to the corresponding sulfoxide and sulfone, respectively. This study demonstrated that 1 acts as stable peroxo carriers that can be discharged and recharged multiple times. An even larger cerium(IV)-peroxo derivative with a tetrameric structure could also be prepared, namely the 12-cerium(IV)-14-peroxo-36-tungsto-4-germanate [CeIV12(O2)14Cl3CeIII(GeW9O34)4]24- (2). In Chapter 4, the synthesis and structural characterization of the sandwich-type cerium(III)-containing 22-tungsto-2-tellurate(VI) [Ce(β2-TeVIW11O39)2]9- (3) is described. In Chapter 5 the synthesis and structu
Computational tools for objective assessment in Neuroimaging
No full textMedical imaging is nowadays capable of non-invasively displaying the human brain in manifold ways. Computer assisted analysis of such data has become a highly active area of research. Today, there exists a wealth of published methods addressing a broad spectrum of medical questions. Considering the maturity to which this field of research has grown by now raises expectations that most basic problems should actually be solved and even many of the more complex task should at least be manageable. However, looking at the role of image-based quantification in everyday clinical practice, draws a completely different picture. The de-facto standard approach in diagnostic radiology is a purely qualitative reading through human experts. Quantification, if used at all, is typically limited to simple measurements on single image-slices. Without debate, there exists a huge gap between what would be potentially possible as defined by the scientific state-of-the-art, and clinical reality.
This PhD thesis addresses this situation. It studies three general concepts aiming at objective image assessment: 1) quantification; 2) interactive segmentation; 3) interactive data-visualization. For each of these concepts, an exemplary application is chosen, and a novel method is proposed with a focus on fulfilling requirements that, if not met, would prevent integration into clinical workflows. First, I present a method for robust assessment of upper-spinal cord atrophy, a parameter which has been successfully correlated to several clinical markers in the context of multiple sclerosis. Second, I present two novel interactive tools for segmenting individual gyri of the brain and regions-of-interest in DTI data. Finally, I present an example of how interactive 3D visualizations combined with efficient tools for exploration of image data can support the planning process of complex neurosurgical interventions
Interrelations of Internet Use and Health Behaviors, Perceived Quality of Life and Work-life Balance: Findings from Web-based studies in Germany and China
No full textA healthy lifestyle plays a key role in maintaining both the quality and the length of life. Interrelation of behaviors (internet use and health behaviors) and higher-level goals (perceived quality of life, work-life balance) are examined in this research.
The first study focuses on the interrelation between internet use and physical activity. While doing so, it identifies the differences across age groups. The second study focuses on the different contributions of work-time and leisure-time internet use to perceived quality of life, taking stress management and health behaviors into account. The third study focuses on the interrelation between multiple health behaviors and work-life balance, as well as the mediator roles of perceived stress and problematic internet use, and the moderator role of the resident countries.
The results of the first study show positive associations between physical activity variables. Positive associations between internet use and physical activity emerges in late adolescents, whereas negative associations between internet use and physical activity planning emerges in middle-aged adults. The results of the second study reveal that leisure-time internet use, but not work-time internet use, is positively associated with problematic internet use. Participants whose work-time internet use could be considered balanced indicates a higher perceived quality of life. The results of the third study indicate the mediator roles of perceived stress and problematic internet use between health behaviors and work-life balance. Among the residents of Germany, a partial mediation is revealed, whereas among the residents of China, a full mediation is found.
Conclusions are given in the form of research, practical and theoretical implications. In today’s digital society, a proper combination of multiple health behaviors and appropriate internet use can benefit individuals’ quality of life and work-life balance
Homotopy Hubbard Trees for Post-Singularly Finite Transcendental Entire Maps
No full textThe main goal of this project is to investigate whether the concept of a Hubbard Tree, well established and widely used in polynomial dynamics, is also meaningful for transcendental entire functions.
For a post-critically finite polynomial, its Hubbard Tree is the unique minimal embedded tree that contains all critical points and is forward invariant under the dynamics of the polynomial (and, in a certain sense, normalized on Fatou components). It is not difficult to adapt this definition to post-singularly finite (psf) transcendental entire maps. We show, however, that there are psf entire maps that do not admit a Hubbard Tree. The reason for this is the existence of asymptotic values.
Partly in order to deal with that issue, we introduce the concept of a Homotopy Hubbard Tree. The essential difference to a Hubbard Tree is that a Homotopy Hubbard Tree is only required to be forward invariant up to homotopy relative to the post-singular set. Our main accomplishment in this work is to show that every psf transcendental entire map admits a Homotopy Hubbard Tree and that this tree is unique up to homotopy relative to the post-singular set.
As a first step towards a classification of psf entire functions in terms of Homotopy Hubbard Trees, we show that a map is uniquely determined by its tree
Supramolecular Sensing Based on Liposomes and Gold Nanoparticles
No full textThe goal of my Ph.D. thesis is the development of supramolecular sensing ensembles based on host-guest complexes for the detection of biological molecules and for monitoring membrane translocation as well as enzymatic transformation. Moreover, these host-guest complexes can be utilized to characterize mixed ligand gold nanoparticles and the deaggregation of perylene-based dyes. The first part of the thesis focuses on the development of novel, robust, simple, and economic fluorescence-based ODC enzyme assay. The second part of the thesis introduces a fluorescence-based biomembrane assay for molecular recognition by the macrocyclic host inside the liposome. In general, supramolecular receptor molecules suffer from low affinity to analytes; therefore, we have introduced a liposome-based sensing approach based on the supramolecular tandem membrane assay principle. The liposome-encapsulated receptor molecules provide higher sensitivity than a homogeneous solution. The third part of the thesis focuses on the determination of membrane permeability and activation energy. Time-resolved monitoring of membrane translocation of analytes is of utmost importance in membrane research. We have introduced a fluorescent artificial receptor membrane assay (FARMA), which is used to monitor in real-time the permeation of indole derivatives through liposomal membrane. FARMA method is a label-free method that enabled the determination of permeation rate, permeability coefficients, and activation energies. The fourth part of the thesis focuses on the characterization of mixed ligand gold nanoparticles and the sensing of the lysine decarboxylase product. In the last part, we report that host-guest complexation affects aggregation of perylene diimide (PDI) dyes, wherein complexation of PDIs by CB7 and CB8 enhances the fluorescence and reduces the self-aggregation of the PDI in aqueous solution