26,165 research outputs found

    Pollution-induced community tolerance in freshwater biofilms ÔÇô from molecular mechanisms to loss of community functions

    Get PDF
    Exposure to herbicides poses a threat to aquatic biofilms by affecting their community structure, physiology and function. These changes render biofilms to become more tolerant, but on the downside community tolerance has ecologic costs. A concept that addresses induced community tolerance to a pollutant (PICT) was introduced by Blanck and W├Ąngberg (1988). The basic principle of the concept is that microbial communities undergo pollution-induced succession when exposed to a pollutant over a long period of time, which changes communities structurally and functionally and enhancing tolerance to the pollutant exposure. However, the mechanisms of tolerance and the ecologic consequences were hardly studied up to date. This thesis addresses the structural and functional changes in biofilm communities and applies modern molecular methods to unravel molecular tolerance mechanisms. Two different freshwater biofilm communities were cultivated for a period of five weeks, with one of the communities being contaminated with 4 ╬╝g L-1 diuron. Subsequently, the communities were characterized for structural and functional differences, especially focusing on their crucial role of photosynthesis. The community structure of the autotrophs was assessed using HPLC-based pigment analysis and their functional alterations were investigated using Imaging-PAM fluorometry to study photosynthesis and community oxygen profiling to determine net primary production. Then, the molecular fingerprints of the communities were measured with meta-transcriptomics (RNA-Seq) and GC-based community metabolomics approaches and analyzed with respect to changes in their molecular functions. The communities were acute exposed to diuron for one hour in a dose-response design, to reveal a potential PICT and uncover related adaptation to diuron exposure. The combination of apical and molecular methods in a dose-response design enabled the linkage of functional effects of diuron exposure and underlying molecular mechanisms based on a sensitivity analysis. Chronic exposure to diuron impaired freshwater biofilms in their biomass accrual. The contaminated communities particularly lost autotrophic biomass, reflected by the decrease in specific chlorophyll a content. This loss was associated with a change in the molecular fingerprint of the communities, which substantiates structural and physiological changes. The decline in autotrophic biomass could be due to a primary loss of sensitive autotrophic organisms caused by the selection of better adapted species in the course of chronic exposure. Related to this hypothesis, an increase in diuron tolerance has been detected in the contaminated communities and molecular mechanisms facilitating tolerance have been found. It was shown that genes of the photosystem, reductive-pentose phosphate cycle and arginine metabolism were differentially expressed among the communities and that an increased amount of potential antioxidant degradation products was found in the contaminated communities. This led to the hypothesis that contaminated communities may have adapted to oxidative stress, making them less sensitive to diuron exposure. Moreover, the photosynthetic light harvesting complex was altered and the photoprotective xanthophyll cycle was increased in the contaminated communities. Despite these adaptation strategies, the loss of autotrophic biomass has been shown to impair primary production. This impairment persisted even under repeated short-term exposure, so that the tolerance mechanisms cannot safeguard primary production as a key function in aquatic systems.:1. The effect of chemicals on organisms and their functions .............................. 1 1.1 Welcome to the anthropocene .......................................................................... 1 1.2 From cellular stress responses to ecosystem resilience ................................... 3 1.2.1 The individual pursuit for homeostasis ....................................................... 3 1.2.2 Stability from diversity ................................................................................. 5 1.3 Community ecotoxicology - a step forward in monitoring the effects of chemical pollution? ................................................................................................................. 6 1.4 Functional ecotoxicological assessment of microbial communities ................... 9 1.5 Molecular tools ÔÇô the key to a mechanistic understanding of stressor effects from a functional perspective in microbial communities? ...................................... 12 2. Aims and Hypothesis ......................................................................................... 14 2.1 Research question .......................................................................................... 14 2.2 Hypothesis and outline .................................................................................... 15 2.3 Experimental approach & concept .................................................................. 16 2.3.1 Aquatic freshwater biofilms as model community ..................................... 16 2.3.2 Diuron as model herbicide ........................................................................ 17 2.3.3 Experimental design ................................................................................. 18 3. Structural and physiological changes in microbial communities after chronic exposure - PICT and altered functional capacity ................................................. 21 3.1 Introduction ..................................................................................................... 21 3.2 Methods .......................................................................................................... 23 3.2.1 Biofilm cultivation ...................................................................................... 23 3.2.2 Dry weight and autotrophic index ............................................................. 23 3.2.4 Pigment analysis of periphyton ................................................................. 23 3.2.4.1 In-vivo pigment analysis for community characterization ....................... 24 3.2.4.2 In-vivo pigment analysis based on Imaging-PAM fluorometry ............... 24 3.2.4.3 In-vivo pigment fluorescence for tolerance detection ............................. 26 3.2.4.4 Ex-vivo pigment analysis by high-pressure liquid-chromatography ....... 27 3.2.5 Community oxygen metabolism measurements ....................................... 28 3.3 Results and discussion ................................................................................... 29 3.3.1 Comparison of the structural community parameters ............................... 29 3.3.2 Photosynthetic activity and primary production of the communities after selection phase ................................................................................................. 33 3.3.3 Acquisition of photosynthetic tolerance .................................................... 34 3.3.4 Primary production at exposure conditions ............................................... 36 3.3.5 Tolerance detection in primary production ................................................ 37 3.4 Summary and Conclusion ........................................................................... 40 4. Community gene expression analysis by meta-transcriptomics ................... 41 4.1 Introduction to meta-transcriptomics ............................................................... 41 4.2. Methods ......................................................................................................... 43 4.2.1 Sampling and RNA extraction................................................................... 43 4.2.2 RNA sequencing analysis ......................................................................... 44 4.2.3 Data assembly and processing................................................................. 45 4.2.4 Prioritization of contigs and annotation ..................................................... 47 4.2.5 Sensitivity analysis of biological processes .............................................. 48 4.3 Results and discussion ................................................................................... 48 4.3.1 Characterization of the meta-transcriptomic fingerprints .......................... 49 4.3.2 Insights into community stress response mechanisms using trend analysis (DRomicÔÇÖs) ......................................................................................................... 51 4.3.3 Response pattern in the isoform PS genes .............................................. 63 4.5 Summary and conclusion ................................................................................ 65 5. Community metabolome analysis ..................................................................... 66 5.1 Introduction to community metabolomics ........................................................ 66 5.2 Methods .......................................................................................................... 68 5.2.1 Sampling, metabolite extraction and derivatisation................................... 68 5.2.2 GC-TOF-MS analysis ............................................................................... 69 5.2.3 Data processing and statistical analysis ................................................... 69 5.3 Results and discussion ................................................................................... 70 5.3.1 Characterization of the metabolic fingerprints .......................................... 70 5.3.2 Difference in the metabolic fingerprints .................................................... 71 5.3.3 Differential metabolic responses of the communities to short-term exposure of diuron ............................................................................................................ 73 5.4 Summary and conclusion ................................................................................ 78 6. Synthesis ............................................................................................................. 79 6.1 Approaches and challenges for linking molecular data to functional measurements ...................................................................................................... 79 6.2 Methods .......................................................................................................... 83 6.2.1 Summary on the data ............................................................................... 83 6.2.2 Aggregation of molecular data to index values (TELI and MELI) .............. 83 6.2.3 Functional annotation of contigs and metabolites using KEGG ................ 83 6.3 Results and discussion ................................................................................... 85 6.3.1 Results of aggregation techniques ........................................................... 85 6.3.2 Sensitivity analysis of the different molecular approaches and endpoints 86 6.3.3 Mechanistic view of the molecular stress responses based on KEGG functions ............................................................................................................ 89 6.4 Consolidation of the results ÔÇô holistic interpretation and discussion ............... 93 6.4.1 Adaptation to chronic diuron exposure - from molecular changes to community effects.............................................................................................. 93 6.4.2 Assessment of the ecological costs of Pollution-induced community tolerance based on primary production ............................................................. 94 6.5 Outlook ............................................................................................................ 9

    What do new performance metrics, VeDBA and Dynamic yaw, tell us about energy-intensive activities in whale sharks?

    Get PDF
    During oscillatory dives, whale sharks (Rhincodon typus) expend varying levels of energy in active ascent and passive descent. They are expected to minimise movement costs by travelling at optimum speed unless having reason to move faster, for example during feeding or evasion of danger. A proxy for power, dynamic body acceleration (DBA) has previously been used to identify whale shark movement patterns but has yet been used to identify occasions where power is elevated above minimum requirements. 59 hours of biologging data from 13 juvenile whale sharks (Ningaloo Reef, Western Australia) including depth, body pitch angle, magnetometry and DBA, was analysed to investigate minimum power requirements for dives and identify events of elevated power. Dynamic yaw (the rate of change of heading), a new proxy for power, was introduced to determine its effectiveness compared to the already-established DBA. The relationship between pitch angle and these two proxies was investigated to determine which had the stronger relationship. Dynamic yaw produced a poor relationship with pitch angle compared to DBA, and thus DBA was selected as the focus proxy for the remainder of the study. DBA was utilised to produce a minimum power trend versus body pitch angle using a convex hull analysis which allowed for the identification of proxy for power utilisation above the minimum (PAM). 16 instances of PAM were identified in 59 hours of data, which could all be considered instances where energy minimisation is not prioritised, such as feeding or avoidance. The PAM method was capable of identifying instances where energy minimisation is not prioritised, and therefore has future implications in investigations of location-specific behaviours in relation to feeding and anthropogenic disturbance

    Complement mediated synapse elimination in schizophrenia

    Get PDF
    Schizophrenia (SCZ) is a devastating psychiatric disorder with a typically age of onset in late adolescence. The heritability is estimated to be in between 60-80% and large-scale genome-wide studies have revealed a prominent polygenic component to SCZ risk and identified more than three-hundred common risk variants. Despite a better understanding of which genetic risk variants that increases SCZ risk, it has been challenging to map out the pathophysiology of the disorder. This has stalled the development of target drugs and current treatment options display moderate efficacy and are prone to produce side-effects. SCZ is generally considered a neurodevelopmental disorder and it was proposed more than forty years ago that physiological removal of less active synapses in adolescence, i.e., synaptic pruning, is increased in SCZ and hereby causes the core symptoms of the disorder. This theory has then been supported by post-mortem brain tissue and imaging studies displaying decreased synapse density in SCZ. More recently, it was then shown that the most strongly associated risk loci can largely be explained by copy numbers of a gene coding for the complement factor 4A (C4A). As microglia prune synapses with the help of complement signalling, we therefore decided to use a recently developed human 2D in vitro assay to assess microglial uptake of synaptic structures in models based on cells from individuals with SCZ and healthy controls (study I). We observed excessive uptake of synaptic structures in SCZ models and by mixing synapses from healthy controls with microglia from SCZ patients, and vice versa, we showed the contribution of microglial and neuronal factors contributing to this excessive uptake of synaptic structures. We then developed an in vitro assay to study neuronal complement deposition dependent on copy numbers of C4A in the neuronal lines. Complement 3 (C3) deposition increased by C4A copy numbers but was independent of C4B copy numbers (also unrelated to SCZ risk). Similar C4A copy numbers correlated with the extent of microglial uptake of synapses. Microglial uptake of synaptic structures could also be inhibited by the tetracycline minocycline that also decreased risk of developing SCZ in an electronic health record cohort. In study II, we cerebrospinal fluid (CSF) from first-episode psychosis patients to measure protein levels of C4A. In two independent cohorts, we observed elevated C4A levels (although not C4B levels) in first-episode patients that later were to develop SCZ and could show correlations with markers of synapse density. However, elevated C4A levels could not fully be explained by more copy numbers of C4A in individuals with SCZ and in vitro experiments revealed that SCZ-associated cytokines can induce C4A mRNA expression while also correlating with C4A in patient-derived CSF. In study III, we set-up a 3D brain organoid models to more fully comprehensively capture processes in the developing human brain and then also included innately developing microglia. We display synaptic pruning within these models and use single cell RNA sequencing to validate them. In conclusion, this thesis uses patient-derived cellular modelling to uncover a disease mechanism in SCZ that link genetic risk variants with bona fide protein changes in living patients

    Anu├írio cient├şfico da Escola Superior de Tecnologia da Sa├║de de Lisboa - 2021

    Get PDF
    ├ë com grande prazer que apresentamos a mais recente edi├ž├úo (a 11.┬¬) do Anu├írio Cient├şfico da Escola Superior de Tecnologia da Sa├║de de Lisboa. Como institui├ž├úo de ensino superior, temos o compromisso de promover e incentivar a pesquisa cient├şfica em todas as ├íreas do conhecimento que contemplam a nossa miss├úo. Esta publica├ž├úo tem como objetivo divulgar toda a produ├ž├úo cient├şfica desenvolvida pelos Professores, Investigadores, Estudantes e Pessoal n├úo Docente da ESTeSL durante 2021. Este Anu├írio ├ę, assim, o reflexo do trabalho ├írduo e dedicado da nossa comunidade, que se empenhou na produ├ž├úo de conte├║do cient├şfico de elevada qualidade e partilhada com a Sociedade na forma de livros, cap├ştulos de livros, artigos publicados em revistas nacionais e internacionais, resumos de comunica├ž├Áes orais e p├│steres, bem como resultado dos trabalhos de 1┬║ e 2┬║ ciclo. Com isto, o conte├║do desta publica├ž├úo abrange uma ampla variedade de t├│picos, desde temas mais fundamentais at├ę estudos de aplica├ž├úo pr├ítica em contextos espec├şficos de Sa├║de, refletindo desta forma a pluralidade e diversidade de ├íreas que definem, e tornam ├║nica, a ESTeSL. Acreditamos que a investiga├ž├úo e pesquisa cient├şfica ├ę um eixo fundamental para o desenvolvimento da sociedade e ├ę por isso que incentivamos os nossos estudantes a envolverem-se em atividades de pesquisa e pr├ítica baseada na evid├¬ncia desde o in├şcio dos seus estudos na ESTeSL. Esta publica├ž├úo ├ę um exemplo do sucesso desses esfor├žos, sendo a maior de sempre, o que faz com que estejamos muito orgulhosos em partilhar os resultados e descobertas dos nossos investigadores com a comunidade cient├şfica e o p├║blico em geral. Esperamos que este Anu├írio inspire e motive outros estudantes, profissionais de sa├║de, professores e outros colaboradores a continuarem a explorar novas ideias e contribuir para o avan├žo da ci├¬ncia e da tecnologia no corpo de conhecimento pr├│prio das ├íreas que comp├Áe a ESTeSL. Agradecemos a todos os envolvidos na produ├ž├úo deste anu├írio e desejamos uma leitura inspiradora e agrad├ível.info:eu-repo/semantics/publishedVersio

    Big Tech and research funding: A bibliometric approach

    Get PDF
    Dissertation presented as the partial requirement for obtaining a Master's degree in Data Science and Advanced Analytics, specialization in Business AnalyticsTechnology companies have radically transformed our daily life in the recent years with help of the wide usage of internet. While transforming our lives, these companies also have grown up even bigger in the recent times and have become more powerful not only financially, but also in terms of computing power and data. Although there have been lots of research done on the influence of large digital economy players (Big Tech) in different fields, the academic influence of these companies is little understood. By drawing on 130,000 academic papers for which there is evidence of support by the Big Tech, the present work applies bibliometric approaches (on the metadata) and text mining techniques (on the contents) to shed a light on the outcomes of this relationship. In particular, we take into consideration research funding (direct strategies) and conference sponsorships (indirect strategies) to empirically explore this relatively unexplored side of Big TechÔÇÖs influence in contemporary society. While developing the analysis a key limitation was the scarcity of prior work exploring the connections between digital platforms and the scientific enterprise. There are several results that come to light from such a perspective, one of these findings is that among the research supported by Big Tech companies, there is big gap between the number of outcomes with the content about the technical perspectives (like machine learning or artificial intelligence) than the content about reflexive (say ethical or environmental) dimensions of innovation, ladder being very small. These findings may stimulate further inquiries into identifying the possible risks, if any, are generated from the direct and indirect financial support by corporate informational giants to academia. The causes and consequences of this non-market activity by companies with big market power may require further attention and research in this field

    Machine Learning Research Trends in Africa: A 30 Years Overview with Bibliometric Analysis Review

    Full text link
    In this paper, a critical bibliometric analysis study is conducted, coupled with an extensive literature survey on recent developments and associated applications in machine learning research with a perspective on Africa. The presented bibliometric analysis study consists of 2761 machine learning-related documents, of which 98% were articles with at least 482 citations published in 903 journals during the past 30 years. Furthermore, the collated documents were retrieved from the Science Citation Index EXPANDED, comprising research publications from 54 African countries between 1993 and 2021. The bibliometric study shows the visualization of the current landscape and future trends in machine learning research and its application to facilitate future collaborative research and knowledge exchange among authors from different research institutions scattered across the African continent

    Bioengineering of Antibody Fragments: Challenges and Opportunities.

    Get PDF
    Antibody fragments are used in the clinic as important therapeutic proteins for treatment of indications where better tissue penetration and less immunogenic molecules are needed. Several expression platforms have been employed for the production of these recombinant proteins, from which E. coli and CHO cell-based systems have emerged as the most promising hosts for higher expression. Because antibody fragments such as Fabs and scFvs are smaller than traditional antibody structures and do not require specific patterns of glycosylation decoration for therapeutic efficacy, it is possible to express them in systems with reduced post-translational modification capacity and high expression yield, for example, in plant and insect cell-based systems. In this review, we describe different bioengineering technologies along with their opportunities and difficulties to manufacture antibody fragments with consideration of stability, efficacy and safety for humans. There is still potential for a new production technology with a view of being simple, fast and cost-effective while maintaining the stability and efficacy of biotherapeutic fragments

    Desarrollo de papeles biocativos por injerto de mol├ęculas espec├şficas en celulosa

    Get PDF
    Tesis (DCI)--FCEFN-UNC, 2019En la presente tesis se presenta el desarrollo de papeles bioactivos con potencial aplicaci├│n en el envasado activo de alimentos. Para tal fin, se propuso el injerto de eugenol, un compuesto de origen natural con propiedades antimicrobiana, antioxidante y repelente de insectos, en celulosa, utilizando ├ícido policarbox├şlico como agente ligante. Con el objetivo de evaluar la escalabilidad del proceso propuesto, se estudiaron distintas tecnolog├şas de curado, tales como calentamiento por convecci├│n, infrarrojo, microondas y conducci├│n. En todos los casos, se analizaron la influencia de las variables operativas sobre el avance de la reacci├│n y propiedades finales del papel preparado, utilizando un dise├▒o de experimentos Doehlert para elegir las experiencias a realizar, y analizando los resultados mediante metodolog├şa de superficie de respuesta y an├ílisis estad├şstico ANOVA. Se pudo comprobar que la reacci├│n de injerto de eugenol en papel comercial se produjo con ├ęxito en todas las tecnolog├şas estudiadas. Asimismo, se encontraron las condiciones ├│ptimas de reacci├│n para cada una de las tecnolog├şas, para lo cual se busc├│ un compromiso entre el avance de la reacci├│n y las propiedades finales del material (mec├ínicas y color). A partir de estas condiciones, se prepararon papeles y se realiz├│ una caracterizaci├│n m├ís espec├şfica para su aplicaci├│n como envase de alimentos comparando los papeles modificados con el papel virgen. Se analizaron las propiedades mec├ínicas por ensayo de tracci├│n, rasgado y punzonado y se midi├│ la absorci├│n de agua y la capacidad de degradaci├│n. Por otro lado, las propiedades bioactivas analizadas fueron la actividad antioxidante, antimicrobiana, repelente e insecticida de gorgojos (T. castaneum y R. dominica). Una vez probado que el papel modificado presenta buenas caracter├şsticas f├şsicas y bioactivas para su posible aplicaci├│n en el envasado de alimentos, se realizaron prototipos de envasado para harina, como alimento representativo de alimentos derivados de cereales, susceptibles al ataque de plagas. En este estudio se analiz├│ la migraci├│n de reactivos, propiedades organol├ępticas y conservaci├│n del alimento, arrojando resultados promisorios para la industria de envases de alimentos. Finalmente, se realiz├│ una comparaci├│n de las tecnolog├şas de curado ensayadas, analizando diferentes aspectos como avance de reacci├│n, propiedades finales, apariencia, tiempo de reacci├│n, consumo de energ├şa, entre otros, como as├ş tambi├ęn disponibilidad y uso de estas tecnolog├şas a escala industrial, seleccionando la tecnolog├şa de conducci├│n como la m├ís adecuada para una propuesta de escalado industrial.Fil: Muratore, Florencia. Universidad Nacional de C├│rdoba. Facultad de Ciencias Exactas, F├şsicas y Naturales; Argentina.Fil: Muratore, Florencia. Consejo Nacional de Investigaciones Cient├şficas y T├ęcnicas. Instituto de Investigaci├│n y Desarrollo en Ingenier├şa de Procesos y Qu├şmica Aplicada; Argentina
    • ÔÇŽ
    corecore