150 research outputs found

    Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae

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    Background Photosynthetic organisms can be used for renewable and sustainable production of fuels and high-value compounds from natural resources. Costs for design and operation of large-scale algae cultivation systems can be reduced if data from laboratory scale cultivations are combined with detailed mathematical models to evaluate and optimize the process. Results In this work we present a flexible modeling formulation for accumulation of high-value storage molecules in microalgae that provides quantitative predictions under various light and nutrient conditions. The modeling approach is based on dynamic flux balance analysis (DFBA) and includes regulatory models to predict the accumulation of pigment molecules. The accuracy of the model predictions is validated through independent experimental data followed by a subsequent model-based fed-batch optimization. In our experimentally validated fed-batch optimization study we increase biomass and β-carotene density by factors of about 2.5 and 2.1, respectively. Conclusions The analysis shows that a model-based approach can be used to develop and significantly improve biotechnological processes for biofuels and pigments

    Theory of branching morphogenesis by local interactions and global guidance

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    Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales

    Molting incidents of Hyalomma spp. carrying human pathogens in Germany under different weather conditions

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    Background Hyalomma marginatum and H. rufipes are two-host tick species, which are mainly distributed in southern Europe, Africa to central Asia but may also be found in Central and Northern Europe through introduction by migratory birds. Methods Ticks were collected while feeding or crawling on animals and humans, or from the environment, in different regions in Germany, between 2019 and 2021 in a citizen science study and from 2022 to 2023 in the wake of this study. Results From 2019 to 2023, a total of 212 Hyalomma adult ticks were detected in Germany. This included 132 H. marginatum and 43 H. rufipes ticks sent to research institutions and 37 photographic records that were only identified to genus level. The number of detected ticks varied over the years, with the highest number of 119 specimens recorded in 2019, followed by 57 in 2020. Most of the specimens were collected from horses, while some were collected from other animals, humans or found crawling on human clothes or other objects inside or outside houses. The screening of 175 specimens for Crimean-Congo hemorrhagic fever virus and of 132 specimens for Babesia/Theileria spp. by PCR gave negative results, while human-pathogenic Rickettsia were detected in 44% (77/175) of the total samples. Subsequent amplicon sequencing and phylogenetic analysis of representative samples determined the species of 41 Rickettsia aeschlimannii and one R. slovaca sequences. Conclusions Analysis of climatic factors indicated a significantly higher probability of Hyalomma occurrence at locations with higher average spring temperature during the years 2019 and 2020 compared to randomly generated pseudo-absence locations. Dry and hot conditions probably facilitated Hyalomma nymphs’ survival and molting into adults during these years

    Breathomics profiling of metabolic pathways affected by major depression: Possibilities and limitations

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    BackgroundMajor depressive disorder (MDD) is one of the most common psychiatric disorders with multifactorial etiologies. Metabolomics has recently emerged as a particularly potential quantitative tool that provides a multi-parametric signature specific to several mechanisms underlying the heterogeneous pathophysiology of MDD. The main purpose of the present study was to investigate possibilities and limitations of breath-based metabolomics, breathomics patterns to discriminate MDD patients from healthy controls (HCs) and identify the altered metabolic pathways in MDD.MethodsBreath samples were collected in Tedlar bags at awakening, 30 and 60 min after awakening from 26 patients with MDD and 25 HCs. The non-targeted breathomics analysis was carried out by proton transfer reaction mass spectrometry. The univariate analysis was first performed by T-test to rank potential biomarkers. The metabolomic pathway analysis and hierarchical clustering analysis (HCA) were performed to group the significant metabolites involved in the same metabolic pathways or networks. Moreover, a support vector machine (SVM) predictive model was built to identify the potential metabolites in the altered pathways and clusters. The accuracy of the SVM model was evaluated by receiver operating characteristics (ROC) analysis.ResultsA total of 23 differential exhaled breath metabolites were significantly altered in patients with MDD compared with HCs and mapped in five significant metabolic pathways including aminoacyl-tRNA biosynthesis (p = 0.0055), branched chain amino acids valine, leucine and isoleucine biosynthesis (p = 0.0060), glycolysis and gluconeogenesis (p = 0.0067), nicotinate and nicotinamide metabolism (p = 0.0213) and pyruvate metabolism (p = 0.0440). Moreover, the SVM predictive model showed that butylamine (p = 0.0005, pFDR=0.0006), 3-methylpyridine (p = 0.0002, pFDR = 0.0012), endogenous aliphatic ethanol isotope (p = 0.0073, pFDR = 0.0174), valeric acid (p = 0.005, pFDR = 0.0162) and isoprene (p = 0.038, pFDR = 0.045) were potential metabolites within identified clusters with HCA and altered pathways, and discriminated between patients with MDD and non-depressed ones with high sensitivity (0.88), specificity (0.96) and area under curve of ROC (0.96).ConclusionAccording to the results of this study, the non-targeted breathomics analysis with high-throughput sensitive analytical technologies coupled to advanced computational tools approaches offer completely new insights into peripheral biochemical changes in MDD

    Update and prognosis of <i>Dermacentor</i> distribution in Germany: Nationwide occurrence of <i>Dermacentor reticulatus</i>.

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    A considerable range expansion of Dermacentor reticulatus has been observed in several European countries, which is concerning in the light of its vector function for several pathogens, including Babesia canis and tick-borne encephalitis virus (TBEV). The present study provides an update on the distribution of Dermacentor ticks in Germany, using a citizen science approach. Ticks were collected by citizens from March 2020 to May 2021, and submitted along with information on the date and location of collection, potential hosts and details about the circumstances of discovery. In total, 3,292 Dermacentor specimens were received, of which 76.4% (2,515/3,292) were identified as D. reticulatus and 23.0% (758/3,292) as D. marginatus, while 0.6% (19/3,292) were too damaged for species-level identification. Dermacentor reticulatus was received from all federal states of Germany. Maxent species distribution models predicted suitable environmental conditions for D. reticulatus throughout Germany. Findings on the vegetation or on pastured animals without travel history confirmed the occurrence of this tick species as far north as the most northern German federal state Schleswig-Holstein. In contrast, the distribution of D. marginatus still appears to be limited to southwestern Germany, although the northward shift of the distribution limit observed in the preceding citizen science study, as compared with previous published distributions, was confirmed. This shift was also predicted by Maxent species distribution models, reflecting the broader distribution of the tick occurrence data contributed by citizens. Most D. reticulatus ticks were found on dogs (1,311/1,960, 66.9%), while D. marginatus was mainly discovered on hoofed animals (197/621, 31.7%) and humans (182/621, 29.3%). Human tick bites were reported in 0.7% (14/1,960) of host-assigned D. reticulatus and 3.4% (21/621) of host-assigned D. marginatus. Further studies to investigate an increasing endemisation of Babesia canis in Germany as well as the relevance of D. reticulatus for TBEV spread throughout the country, e.g., by traveling dogs, are urgently needed. In view of the activity of D. reticulatus during winter or the colder months, which complements that of Ixodes ricinus, a year-round tick protection of at least dogs is strongly recommended

    Characterization of a polychromatic microfocus X-ray fluorescence imaging setup with metallic contrast agents in a microphysiological tumor model

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    Introduction: Accurate diagnosis and personalized treatments involving site-targeted cancer localization, drug delivery, therapeutic strategy, and disease pathways identification, rely on a precise understanding of biomarker kinetics, drug pharmacokinetics, and mechanistic behaviour of functionalized tracers through in vitro and in vivo studies. X-ray fluorescence (XRF) computed tomography (XFCT) offers a potential alternative to current 3D imaging techniques for spatiotemporal localization of nanoparticle-tracers with high spatial resolution and sensitivity. In this work, the applicability of a benchtop cone-beam system with a polychromatic X-ray source was examined with regard to physical constraints of engineered tissue models. Methods: A tissue engineering approach based on a decellularized scaffold was used to establish a 3D breast cancer model with MDA-MB-231 cells in co-culture with primary human fibroblasts. The 3D breast cancer system, in combination with small-animal-sized phantoms, was used to demonstrate the novel integrated pre-clinical imaging approach to perform in vitro surrogate investigations and non-destructive analysis on biophantoms. These models are adopted to evaluate the functionality and optimize the setup for high-spatial-resolution, fast, and fully-3D quantitative imaging. Polychromatic X-rays from a microfocus source are used for XRF stimulation from conventional Gadolinium (Gd) and nanoparticle-based Molybdenum (MoNPs) contrast agents. Results and Discussion: The intestinal scaffold allowed the invasion of the breast cancer cells over this barrier and therefore provides a valuable tool to study metastasis formation of tumor cells from epithelial origin. The breast cancer model was well suited for the development and validation of the proposed XRF imaging, with spatial resolution under <2 mm and contrast dose in the order of a few 100 μg/mL (∼0.3 mg/mL for Gd and ∼0.5 mg/mL for MoNPs), radiation dose in the order of a few 100 cGy (280 cGy for Gd and 94 cGy for MoNPs, with a possible reduction of an order of magnitude for Gd and 67% for MoNPs), and imaging time in the order of 10 min for Gd (33 min total) and 100 min (2.8 h total) for MoNPs, approaching in vivo conform conditions for pre-clinical studies. High-resolution XFCT for tissue-engineered cancer models would be of significant interest in biomedical research and diagnostic imaging, e.g., for an increased mechanistic understanding of molecular processes in tumor formation or early cancer detection
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