26,909 research outputs found

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

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    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 Wängberg (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 μg 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 – 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 (DRomic’s) ......................................................................................................... 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 – 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

    Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy

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    UFMylation involves the covalent modification of substrate proteins with UFM1 (Ubiquitin‐fold modifier 1) and is important for maintaining ER homeostasis. Stalled translation triggers the UFMylation of ER‐bound ribosomes and activates C53‐mediated autophagy to clear toxic polypeptides. C53 contains noncanonical shuffled ATG8‐interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. However, the mechanistic basis of sAIM‐mediated ATG8 interaction remains unknown. Here, we show that C53 and sAIMs are conserved across eukaryotes but secondarily lost in fungi and various algal lineages. Biochemical assays showed that the unicellular alga Chlamydomonas reinhardtii has a functional UFMylation pathway, refuting the assumption that UFMylation is linked to multicellularity. Comparative structural analyses revealed that both UFM1 and ATG8 bind sAIMs in C53, but in a distinct way. Conversion of sAIMs into canonical AIMs impaired binding of C53 to UFM1, while strengthening ATG8 binding. Increased ATG8 binding led to the autoactivation of the C53 pathway and sensitization of Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral role of sAIMs in UFMylation‐dependent fine‐tuning of C53‐mediated autophagy activation

    Big Tech and research funding: A bibliometric approach

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    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 Tech’s 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

    Neuroanatomical and gene expression features of the rabbit accessory olfactory system. Implications of pheromone communication in reproductive behaviour and animal physiology

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    Mainly driven by the vomeronasal system (VNS), pheromone communication is involved in many species-specific fundamental innate socio-sexual behaviors such as mating and fighting, which are essential for animal reproduction and survival. Rabbits are a unique model for studying chemocommunication due to the discovery of the rabbit mammary pheromone, but paradoxically there has been a lack of knowledge regarding its VNS pathway. In this work, we aim at filling this gap by approaching the system from an integrative point of view, providing extensive anatomical and genomic data of the rabbit VNS, as well as pheromone-mediated reproductive and behavioural studies. Our results build strong foundation for further translational studies which aim at implementing the use of pheromones to improve animal production and welfare

    Wooster Magazine: Spring 2023

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    The spring 2023 issue of Wooster magazine features alumni influencing change in their communities around the world, including John Carwile ’81, career member of the U.S. Foreign Service; Rashmi Ekka ’08, international development consultant; Samira El-Adawy ’13, Special Olympics youth manager in the Middle East and North Africa; Ishtiaq Ghafoor ’00, a diplomat with the British Foreign Service; Sarah Haile ’03, a biostatistician at University of Zurich; Kurt Russell ’94, 2022 National Teacher of the Year; and Lauren Vargo ’13, climate change researcher in New Zealand. Also featured are students who have attended the annual Athens Democracy Forum for the past five years and recent international graduates taking advantage of opportunities to gain experience in STEM fields. The issue also includes an interview with Wooster’s incoming 13th president, Dr. Anne McCall.https://openworks.wooster.edu/wooalumnimag_2011-present/1045/thumbnail.jp

    OLIG2 neural progenitor cell development and fate in Down syndrome

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    Down syndrome (DS) is caused by triplication of human chromosome 21 (HSA21) and is the most common genetic form of intellectual disability. It is unknown precisely how triplication of HSA21 results in the intellectual disability, but it is thought that the global transcriptional dysregulation caused by trisomy 21 perturbs multiple aspects of neurodevelopment that cumulatively contribute to its etiology. While the characteristics associated with DS can arise from any of the genes triplicated on HSA21, in this work we focus on oligodendrocyte transcription factor 2 (OLIG2). The progeny of neural progenitor cells (NPCs) expressing OLIG2 are likely to be involved in many of the cellular changes underlying the intellectual disability in DS. To explore the fate of OLIG2+ neural progenitors, we took advantage of two distinct models of DS, the Ts65Dn mouse model and induced pluripotent stem cells (iPSCs) derived from individuals with DS. Our results from these two systems identified multiple perturbations in development in the cellular progeny of OLIG2+ NPCs. In Ts65Dn, we identified alterations in neurons and glia derived from the OLIG2 expressing progenitor domain in the ventral spinal cord. There were significant differences in the number of motor neurons and interneurons present in the trisomic lumbar spinal cord depending on age of the animal pointing both to a neurodevelopment and a neurodegeneration phenotype in the Ts65Dn mice. Of particular note, we identified changes in oligodendrocyte (OL) maturation in the trisomic mice that are dependent on spatial location and developmental origin. In the dorsal corticospinal tract, there were significantly fewer mature OLs in the trisomic mice, and in the lateral funiculus we observed the opposite phenotype with more mature OLs being present in the trisomic animals. We then transitioned our studies into iPSCs where we were able to pattern OLIG2+ NPCs to either a spinal cord-like or a brain-like identity and study the OL lineage that differentiated from each progenitor pool. Similar to the region-specific dysregulation found in the Ts65Dn spinal cord, we identified perturbations in trisomic OLs that were dependent on whether the NPCs had been patterned to a brain-like or spinal cord-like fate. In the spinal cord-like NPCs, there was no difference in the proportion of cells expressing either OLIG2 or NKX2.2, the two transcription factors whose co-expression is essential for OL differentiation. Conversely, in the brain-like NPCs, there was a significant increase in OLIG2+ cells in the trisomic culture and a decrease in NKX2.2 mRNA expression. We identified a sonic hedgehog (SHH) signaling based mechanism underlying these changes in OLIG2 and NKX2.2 expression in the brain-like NPCs and normalized the proportion of trisomic cells expressing the transcription factors to euploid levels by modulating the activity of the SHH pathway. Finally, we continued the differentiation of the brain-like and spinal cord-like NPCs to committed OL precursor cells (OPCs) and allowed them to mature. We identified an increase in OPC production in the spinal cord-like trisomic culture which was not present in the brain-like OPCs. Conversely, we identified a maturation deficit in the brain-like trisomic OLs that was not present in the spinal cord-like OPCs. These results underscore the importance of regional patterning in characterizing changes in cell differentiation and fate in DS. Together, the findings presented in this work contribute to the understanding of the cellular and molecular etiology of the intellectual disability in DS and in particular the contribution of cells differentiated from OLIG2+ progenitors

    Therapeutic effect of mesenchymal stem cell derived extracellular vesicles on 3D model of oligocortical spheroids

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    Extracellular vesicles (EVs) are released by nearly every cell type and are an important structure in inter-cellular communication. Abnormal EV signaling is found in many conditions including ischemia, Alzheimer’s Disease (AD) and Down Syndrome (DS). However, EVs from stem cells from healthy animals have recently emerged as a possible therapeutic intervention to address a variety of neurological conditions. Mesenchymal stromal cell-derived (MSCs) extracellular vesicles from the bone marrow of young healthy monkeys contain microRNAs and proteins and previous studies have shown that MSC-EV treatment mitigates inflammation and oxidative stress, promotes myelination, and improves functional recovery in a rhesus monkey model of cortical injury. EVs have also been shown to reduce AD pathology in mouse models by promoting anti-inflammatory processes and slowing the progression of AD. While AD currently effects over 6 million people in the United States, individuals with DS are disproportionately affected by early onset AD. Therefore, investigating the efficacy of MSC-EVs as a potential therapeutic to mitigate AD like pathology in DS is critical. Accordingly, the current study aims to explore the application of EVs on 3D human brain models of DS, ischemia, and oxygen glucose deprivation (OGD). We generated human oligocortical spheroids (OLS) containing neurons, astrocytes and oligodendrocytes allowing investigation of the effects of the EVs in human, physiologically relevant conditions. First, with OLS in ischemic conditions results were insufficient in demonstrating the recapitulation of cell death and oxidative damage associated with ischemia in vivo. Consequently, the inconsistency of the model prevented us from comprehensive evaluation of the therapeutic potential of EVs in OGD model in OLS. However, we next used DS-derived OLS generated from isogenic induced pluripotent stem cell (iPSCs) lines to evaluate the efficacy of EV treatment in DS. Trisomic OLS display significantly higher levels of amyloid beta (Aβ40 and Aβ42) depositions in both the soluble and insoluble fractions. Additionally, trisomic OLS are consistently smaller than their euploid counterparts, and have elevated levels of cleaved-caspase 3 (CC3) detection indicating more cell death. When treated with EVs, trisomic OLS demonstrated greater preserved cortical volume, significantly decreased levels of Aβ40 and Aβ42 in both fractions, and significant reduction in cell death compared to the untreated trisomic OLS. These results suggest that EVs alleviated the AD-related pathology in DS-derived OLS. Evaluation of the markers of cortical layer neurons demonstrated significantly higher counts of neurons expressing deep and superficial layer markers, suggesting that EVs contributed to greater preserved cortical volume of trisomic OLS by promoting neurogenesis and alleviating trisomy-induced deficits. Our studies show for the first time the efficacy of MSC-EVs in mitigating DS and AD-related cellular phenotypes and pathological depositions in human OLS. Furthermore, oligocortical spheroids present a unique tool for a target validation of potential therapeutics

    Understanding interactions between Ramularia collo-cygni and barley leaf physiology to target improvements in host resistance and disease control strategy

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    Ramularia Leaf Spot (RLS) is an increasingly problematic disease of barley. Control options are limited as the causal fungus, Ramularia collo-cygni, has developed resistance to several of the major fungicide groups. Developing new methods for controlling this disease is therefore a priority. R. collo-cygni can grow systemically in barley plants from infected seed, without inducing visible symptoms. In the field, visible symptoms normally only appear after flowering. The relative contribution of the latent and symptomatic stages of the fungal lifecycle to reduction in barley yield is not currently known with any certainty. Two possibilities are that the effect of asymptomatic infection on pre-flowering photosynthetic activity, and the development of grain sink capacity, plays an important role; or that reduction in photosynthetic activity during grain filling, resulting from lesion development and loss of green leaf area, is the predominant factor. This research aimed to increase our understanding of the impact of different phases of the fungal lifecycle on barley photosynthesis and yield formation, to better target host resistance and disease control strategies. Controlled environment and field experiments were used to determine the relative effects of asymptomatic and symptom-expressing phases of R. collo-cygni infection on photosynthesis and yield formation in spring barley. In controlled environment experiments leaf photosynthetic activity was measured in seedlings inoculated with suspensions of R. collo-cygni mycelia. Measurements were made before and after visible symptom development using Infra-Red Gas Analysis (IRGA), chlorophyll fluorescence analysis and chlorophyll fluorescence imaging. No reduction in photosynthetic activity was observed in leaves infected with R. collo-cygni, compared to those of non- infected leaves, during the latent phase of infection. After the appearance of visible symptoms, photosynthetic activity within lesions reduced as the lesions developed. However, this did not lead to reductions in photosynthetic activity when measured across the whole leaf area, suggesting that for there to be a significant effect of disease on whole leaf photosynthetic activity, visible symptoms must develop into mature lesions and coalesce to cover larger areas of the leaf surface. In field experiments plots were treated with a full fungicide regime, left untreated, or inoculated with R. collo-cygni and treated with fungicide to which R. collo-cygni is resistant (the latter as a precaution against lack of natural RLS disease that year and/or other diseases developing on untreated plots). RLS was the only disease of significance that developed in untreated or inoculated plots. Symptoms first appeared after flowering, around Zadoks Growth Stage 72. Fungicide-treated plots remained free of disease. Chlorophyll fluorescence analysis of field plants showed no effect of infection on the maximum quantum efficiency of Photosystem II (Fv/Fm) before visible symptom development, consistent with results from controlled environment experiments. Grain yield of untreated and fungicide-treated plots was predicted from fixed common values of radiation use efficiency (RUE) and utilisation of soluble sugar reserves, and measured values of post-flowering healthy (green) leaf area light interception. Grain yields predicted from the difference in post-flowering light interception between fungicide-treated plants and untreated or inoculated plants displaying symptoms of RLS were comparable with the measured yield response to fungicide. This suggests that yield loss to RLS is primarily associated with a reduction in light capture during grain filling, resulting from lesion development and loss of green leaf area. Results from controlled environment and field experiments suggested that symptom expression was associated with leaf senescence. Further controlled environment experiments tested this relationship by using treatments to vary the onset and rate of leaf senescence. Seedlings that were treated with cytokinin to delay senescence after inoculation with suspensions of R. collo-cygni mycelia developed fewer lesions than control plants. Fungal growth, as measured by quantification of R. collo-cygni DNA in leaves, was also restricted in plants treated with cytokinin. Collectively these results suggest that prevention of visible symptom development, rather than prevention of asymptomatic growth, is the most important target for management of this disease. Control methods targeted at delaying senescence could be a useful avenue for further investigation
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