18,103 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

    Identifizierung pr├Ądiktiver und prognostischer Biomarker in unterschiedlichen Tumorkompartimenten des ├Âsophagealen Adenokarzinoms

    Get PDF
    Das ├Âsophageale Adenokarzinom zeigt eine global steigende Inzidenz und hat mit einer 5-Jahres-├ťberlebensrate von weniger als 25% eine schlechte Prognose. Personalisierte Therapieans├Ątze sind selten und prognostische/pr├Ądiktive Biomarker des Tumormikromilieus sind unzureichend charakterisiert. Die kumulative Promotion n├Ąhert sich dieser Problematik in drei unterschiedlichen Schwerpunkten. 1. Zur Identifizierung Kompartiment-spezifischer Biomarker wurde eine Methode entwickelt, welche als kosteng├╝nstige Alternative zum sc-Seq Expressionsprofile individueller Zelltypen generiert. Dabei erfolgt die Extraktion der RNA nicht aus Einzelzellen, sondern aus flowzytometrisch-getrennten Zellkompartimenten. Die Separation der Proben in Epithelzellen, Immunzellen und Fibroblasten wurde durch verschiedene Verfahren validiert und eine suffiziente Ausbeute an RNA auch f├╝r kleine Gewebemengen gezeigt. 2. Biomarker des Immunzellkompartiments als therapeutische Angriffspunkte wurden in einem Patientenkollektiv von bis zu 551 Patienten auf ihre Bedeutung beim EAC ├╝berpr├╝ft. Es zeigte sich eine Expression der Immuncheckpoints LAG3, VISTA und IDO auf TILs durch IHC und RNA-Sonden basierte Verfahren in einem relevanten Anteil (LAG3: 11,4%, VISTA: 29%, IDO: 52,6%). Es konnte eine prognostisch g├╝nstige Bedeutung der VISTA, LAG3 und IDO Expression gezeigt werden. Durch den Vergleich von Genexpressionsprofilen aus therapienaiven und vorbehandelten Tumoren konnte zudem ein immunsuppressiver Effekt von neoadjuvanten Therapiekonzepten auf das Tumormikromilieu des EACs gezeigt werden. Dabei kam es zur verminderten Expression von Checkpoints und Anzahl TILs nach (Radio-) Chemotherapie. 3. Im Tumorzellkompartiment wurde die Rolle von Amplifikationen in ErbB-Rezeptor abh├Ąngigen Signalwegen durch FISH-Technik und Immunhistochemie evaluiert. Es fanden sich KRAS Amplifikationen in 17,1%, PIK3CA Amplifikationen in 5% sowie eine HER2/neu-├ťberexpression in 14,9% der untersuchten Tumore

    Annual SHOT Report 2018

    Get PDF
    SHOT is affiliated to the Royal College of PathologistsAll NHS organisations must move away from a blame culture towards a just and learning culture. All clinical and laboratory staff should be encouraged to become familiar with human factors and ergonomics concepts. All transfusion decisions must be made after carefully assessing the risks and benefits of transfusion therapy. Collaboration and co-ordination among staff is vital

    Examples of works to practice staccato technique in clarinet instrument

    Get PDF
    Klarnetin staccato tekni─čini g├╝├žlendirme a┼čamalar─▒ eser ├žal─▒┼čmalar─▒yla uygulanm─▒┼čt─▒r. Staccato ge├ži┼člerini h─▒zland─▒racak ritim ve n├╝ans ├žal─▒┼čmalar─▒na yer verilmi┼čtir. ├çal─▒┼čman─▒n en ├Ânemli amac─▒ sadece staccato ├žal─▒┼čmas─▒ de─čil parmak-dilin e┼č zamanl─▒ uyumunun hassasiyeti ├╝zerinde de durulmas─▒d─▒r. Staccato ├žal─▒┼čmalar─▒n─▒ daha verimli hale getirmek i├žin eser ├žal─▒┼čmas─▒n─▒n i├žinde et├╝t ├žal─▒┼čmas─▒na da yer verilmi┼čtir. ├çal─▒┼čmalar─▒n ├╝zerinde titizlikle durulmas─▒ staccato ├žal─▒┼čmas─▒n─▒n ilham verici etkisi ile m├╝zikal kimli─če yeni bir boyut kazand─▒rm─▒┼čt─▒r. Sekiz ├Âzg├╝n eser ├žal─▒┼čmas─▒n─▒n her a┼čamas─▒ anlat─▒lm─▒┼čt─▒r. Her a┼čaman─▒n bir sonraki performans ve tekni─či g├╝├žlendirmesi esas al─▒nm─▒┼čt─▒r. Bu ├žal─▒┼čmada staccato tekni─činin hangi alanlarda kullan─▒ld─▒─č─▒, nas─▒l sonu├žlar elde edildi─či bilgisine yer verilmi┼čtir. Notalar─▒n parmak ve dil uyumu ile nas─▒l ┼čekillenece─či ve nas─▒l bir ├žal─▒┼čma disiplini i├žinde ger├žekle┼čece─či planlanm─▒┼čt─▒r. Kam─▒┼č-nota-diyafram-parmak-dil-n├╝ans ve disiplin kavramlar─▒n─▒n staccato tekni─činde ayr─▒lmaz bir b├╝t├╝n oldu─ču saptanm─▒┼čt─▒r. Ara┼čt─▒rmada literat├╝r taramas─▒ yap─▒larak staccato ile ilgili ├žal─▒┼čmalar taranm─▒┼čt─▒r. Tarama sonucunda klarnet tekni─čin de kullan─▒lan staccato eser ├žal─▒┼čmas─▒n─▒n az oldu─ču tespit edilmi┼čtir. Metot taramas─▒nda da et├╝t ├žal─▒┼čmas─▒n─▒n daha ├žok oldu─ču saptanm─▒┼čt─▒r. B├Âylelikle klarnetin staccato tekni─čini h─▒zland─▒rma ve g├╝├žlendirme ├žal─▒┼čmalar─▒ sunulmu┼čtur. Staccato et├╝t ├žal─▒┼čmalar─▒ yap─▒l─▒rken, araya eser ├žal─▒┼čmas─▒n─▒n girmesi beyni rahatlatt─▒─č─▒ ve isteklili─či daha artt─▒rd─▒─č─▒ g├Âzlemlenmi┼čtir. Staccato ├žal─▒┼čmas─▒n─▒ yaparken do─čru bir kam─▒┼č se├žimi ├╝zerinde de durulmu┼čtur. Staccato tekni─čini do─čru ├žal─▒┼čmak i├žin do─čru bir kam─▒┼č─▒n dil h─▒z─▒n─▒ artt─▒rd─▒─č─▒ saptanm─▒┼čt─▒r. Do─čru bir kam─▒┼č se├žimi kam─▒┼čtan rahat ses ├ž─▒kmas─▒na ba─čl─▒d─▒r. Kam─▒┼č, dil atma g├╝c├╝n├╝ vermiyorsa daha do─čru bir kam─▒┼č se├žiminin yap─▒lmas─▒ gereklili─či vurgulanm─▒┼čt─▒r. Staccato ├žal─▒┼čmalar─▒nda ba┼čtan sona bir eseri yorumlamak zor olabilir. Bu a├ž─▒dan ├žal─▒┼čma, verilen m├╝zikal n├╝anslara uyman─▒n, dil at─▒┼č performans─▒n─▒ rahatlatt─▒─č─▒n─▒ ortaya koymu┼čtur. Gelecek nesillere edinilen bilgi ve birikimlerin aktar─▒lmas─▒ ve geli┼čtirici olmas─▒ te┼čvik edilmi┼čtir. ├ç─▒kacak eserlerin nas─▒l ├ž├Âz├╝lece─či, staccato tekni─činin nas─▒l ├╝stesinden gelinebilece─či anlat─▒lm─▒┼čt─▒r. Staccato tekni─činin daha k─▒sa s├╝rede ├ž├Âz├╝me kavu┼čturulmas─▒ ama├ž edinilmi┼čtir. Parmaklar─▒n yerlerini ├Â─čretti─čimiz kadar belle─čimize de ├žal─▒┼čmalar─▒n kaydedilmesi ├Ânemlidir. G├Âsterilen azmin ve sabr─▒n sonucu olarak ortaya ├ž─▒kan yap─▒t ba┼čar─▒y─▒ daha da yukar─▒ seviyelere ├ž─▒karacakt─▒r

    Immunosuppressive drugs in renal transplantation

    Get PDF
    A kidney transplant, sometimes known as a renal transplant, is the treatment of choice for kidney failure at end stage renal disease (ESRD). The renal transplant surgery is followed by a lifetime course of immunosuppressive agents, divided into initial induction phase and later maintenance phase. It is seen that the risk of acute rejection is maximum in the initial months after transplantation (induction phase) and then reduces later (maintenance phase). In induction phase there is use of high-intensity immunosuppression immediately after transplantation, when the risk of rejection is maximum and then the dose reduced for long- term therapy. The main challenge in the renal transplantation community is long- term transplant survival. Long-term graft loss is mainly due to acute and chronic graft rejection, and also due to complications of immunosuppressive therapy. Currently, there is triple therapy as conventional immunosuppressive protocol: a calcineurin inhibitor, an antimetabolite agent, and a corticosteroid. The main aim of development of new immunosuppressive agents is not only improvement of short- term outcomes but also to increase the long- term graft survival by less nephrotoxicity, and minimal side-effects

    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

    Similarity and variability of blocked weather-regime dynamics in the AtlanticÔÇôEuropean region

    Get PDF
    Weather regimes govern an important part of the sub-seasonal variability of the mid-latitude circulation. Due to their role in weather extremes and atmospheric predictability, regimes that feature a blocking anticyclone are of particular interest. This study investigates the dynamics of these ÔÇťblockedÔÇŁ regimes in the North AtlanticÔÇôEuropean region from a year-round perspective. For a comprehensive diagnostic, wave activity concepts and a piecewise potential vorticity┬á(PV) tendency framework are combined. The latter essentially quantifies the well-established PV┬áperspective of mid-latitude dynamics. The four blocked regimes (namely Atlantic ridge, European blocking, Scandinavian blocking, and Greenland blocking) during the 1979ÔÇô2021 period of ERA5 reanalysis are considered. Wave activity characteristics exhibit distinct differences between blocked regimes. After regime onset, Greenland blocking is associated with a suppression of wave activity flux, whereas Atlantic ridge and European blocking are associated with a northward deflection of the flux without a clear net change. During onset, the envelope of Rossby wave activity retracts upstream for Greenland blocking, whereas the envelope extends downstream for Atlantic ridge and European blocking. Scandinavian blocking exhibits intermediate wave activity characteristics. From the perspective of piecewise PV┬átendencies projected onto the respective regime pattern, the dynamics that govern regime onset exhibit a large degree of similarity: linear Rossby wave dynamics and nonlinear eddy PV┬áfluxes dominate and are of approximately equal relative importance, whereas baroclinic coupling and divergent amplification make minor contributions. Most strikingly, all blocked regimes exhibit very similar (intra-regime) variability: a retrograde and an upstream pathway to regime onset. The retrograde pathway is dominated by nonlinear PV┬áeddy fluxes, whereas the upstream pathway is dominated by linear Rossby wave dynamics. Importantly, there is a large degree of cancellation between the two pathways for some of the mechanisms before regime onset. The physical meaning of a regime-mean perspective before onset can thus be severely limited. Implications of our results for understanding predictability of blocked regimes are discussed. Further discussed are the limitations of projected tendencies in capturing the importance of moist-baroclinic growth, which tends to occur in regions where the amplitude of the regime pattern, and thus the projection onto it, is small. Finally, it is stressed that this study investigates the variability of the governing dynamics without prior empirical stratification of data by season or by type of regime transition. It is demonstrated, however, that our dynamics-centered approach does not merely reflect variability that is associated with these factors. The main modes of dynamical variability revealed herein and the large similarity of the blocked regimes in exhibiting this variability are thus significant results.</p

    A Decision Support System for Economic Viability and Environmental Impact Assessment of Vertical Farms

    Get PDF
    Vertical farming (VF) is the practice of growing crops or animals using the vertical dimension via multi-tier racks or vertically inclined surfaces. In this thesis, I focus on the emerging industry of plant-specific VF. Vertical plant farming (VPF) is a promising and relatively novel practice that can be conducted in buildings with environmental control and artificial lighting. However, the nascent sector has experienced challenges in economic viability, standardisation, and environmental sustainability. Practitioners and academics call for a comprehensive financial analysis of VPF, but efforts are stifled by a lack of valid and available data. A review of economic estimation and horticultural software identifies a need for a decision support system (DSS) that facilitates risk-empowered business planning for vertical farmers. This thesis proposes an open-source DSS framework to evaluate business sustainability through financial risk and environmental impact assessments. Data from the literature, alongside lessons learned from industry practitioners, would be centralised in the proposed DSS using imprecise data techniques. These techniques have been applied in engineering but are seldom used in financial forecasting. This could benefit complex sectors which only have scarce data to predict business viability. To begin the execution of the DSS framework, VPF practitioners were interviewed using a mixed-methods approach. Learnings from over 19 shuttered and operational VPF projects provide insights into the barriers inhibiting scalability and identifying risks to form a risk taxonomy. Labour was the most commonly reported top challenge. Therefore, research was conducted to explore lean principles to improve productivity. A probabilistic model representing a spectrum of variables and their associated uncertainty was built according to the DSS framework to evaluate the financial risk for VF projects. This enabled flexible computation without precise production or financial data to improve economic estimation accuracy. The model assessed two VPF cases (one in the UK and another in Japan), demonstrating the first risk and uncertainty quantification of VPF business models in the literature. The results highlighted measures to improve economic viability and the viability of the UK and Japan case. The environmental impact assessment model was developed, allowing VPF operators to evaluate their carbon footprint compared to traditional agriculture using life-cycle assessment. I explore strategies for net-zero carbon production through sensitivity analysis. Renewable energies, especially solar, geothermal, and tidal power, show promise for reducing the carbon emissions of indoor VPF. Results show that renewably-powered VPF can reduce carbon emissions compared to field-based agriculture when considering the land-use change. The drivers for DSS adoption have been researched, showing a pathway of compliance and design thinking to overcome the ÔÇśproblem of implementationÔÇÖ and enable commercialisation. Further work is suggested to standardise VF equipment, collect benchmarking data, and characterise risks. This work will reduce risk and uncertainty and accelerate the sectorÔÇÖs emergence
    • ÔÇŽ
    corecore