Showing papers by "University of Düsseldorf published in 2023"

Genotype–environment interactions determine microbiota plasticity in the sea anemone Nematostella vectensis

Abstract: Most multicellular organisms harbor microbial colonizers that provide various benefits to their hosts. Although these microbial communities may be host species- or even genotype-specific, the associated bacterial communities can respond plastically to environmental changes. In this study, we estimated the relative contribution of environment and host genotype to bacterial community composition in Nematostella vectensis, an estuarine cnidarian. We sampled N. vectensis polyps from 5 different populations along a north-south gradient on the Atlantic coast of the United States and Canada. In addition, we sampled 3 populations at 3 different times of the year. While half of the polyps were immediately analyzed for their bacterial composition by 16S rRNA gene sequencing, the remaining polyps were cultured under laboratory conditions for 1 month. Bacterial community comparison analyses revealed that laboratory maintenance reduced bacterial diversity by 4-fold, but maintained a population-specific bacterial colonization. Interestingly, the differences between bacterial communities correlated strongly with seasonal variations, especially with ambient water temperature. To decipher the contribution of both ambient temperature and host genotype to bacterial colonization, we generated 12 clonal lines from 6 different populations in order to maintain each genotype at 3 different temperatures for 3 months. The bacterial community composition of the same N. vectensis clone differed greatly between the 3 different temperatures, highlighting the contribution of ambient temperature to bacterial community composition. To a lesser extent, bacterial community composition varied between different genotypes under identical conditions, indicating the influence of host genotype. In addition, we identified a significant genotype x environment interaction determining microbiota plasticity in N. vectensis. From our results we can conclude that N. vectensis-associated bacterial communities respond plastically to changes in ambient temperature, with the association of different bacterial taxa depending in part on the host genotype. Future research will reveal how this genotype-specific microbiota plasticity affects the ability to cope with changing environmental conditions.

Attack of the snowclones: A corpus-based analysis of extravagant formulaic patterns

Abstract: The concept of ‘snowclones’ has gained interest in recent research on linguistic creativity and in studies of extravagance and expressiveness in language. However, no clear criteria for identifying snowclones have yet been established, and detailed corpus-based investigations of the phenomenon are still lacking. This paper addresses this research gap in a twofold way. On the one hand, we develop an operational definition of snowclones, arguing that three criteria are decisive: (i) the existence of a lexically fixed source construction; (ii) partial productivity; (iii) ‘extravagant’ formal and/or functional characteristics. On the other hand, we offer an empirical investigation of two patterns that have often been mentioned as examples of snowclones in the previous literature, namely [ the mother of all X] and [X BE the new Y]. We use collostructional analysis and distributional semantics to explore the partial productivity of both patterns’ slot fillers. In sum, we argue that the concept of snowclones, if properly defined, can contribute substantially to our understanding of creative language use, especially regarding the question of how social, cultural, and interpersonal factors influence the choice of more or less salient linguistic constructions.

Compression of colloidal monolayers at liquid interfaces: <i>in situ vs. ex situ</i> investigation

Abstract: The assembly of colloidal particles at liquid interfaces is a versatile procedure to create microstructured monolayers. Our in situ small-angle light scattering of the monolayer provides new insights into the interfacial assembly behavior.

Gene expression studies of WT1 mutant Wilms tumor cell lines in the frame work of published kidney development data reveals their early kidney stem cell origin

Abstract: In order to get a better insight into the timing of WT1 mutant Wilms tumor development, we compared the gene expression profiles of nine established WT1 mutant Wilms tumor cell lines with published data from different kidney cell types during development. Publications describing genes expressed in nephrogenic precursor cells, ureteric bud cells, more mature nephrogenic epithelial cells and interstitial cell types were used. These studies uncovered that the WT1 mutant Wilms tumor cells lines express genes from the earliest nephrogenic progenitor cells, as well as from more differentiated nephron cells with the highest expression from the stromal/interstitial compartment. The expression of genes from all cell compartments points to an early developmental origin of the tumor in a common stem cell. Although variability of the expression of specific genes was evident between the cell lines the overall expression pattern was very similar. This is likely dependent on their different genetic backgrounds with distinct WT1 mutations and the absence/presence of mutant CTNNB1.

The angular gyrus serves as an interface between the non-lexical reading network and the semantic system: evidence from dynamic causal modeling

Abstract: Understanding encoded language, such as written words, requires multiple cognitive processes that act in a parallel and interactive fashion. These processes and their interactions, however, are not fully understood. Various conceptual and methodical approaches including computational modeling and neuroimaging have been applied to better understand the neural underpinnings of these complex processes in the human brain. In this study, we tested different predictions of cortical interactions that derived from computational models for reading using dynamic causal modeling. Morse code was used as a model for non-lexical decoding followed by a lexical-decision during a functional magnetic resonance examination. Our results suggest that individual letters are first converted into phonemes within the left supramarginal gyrus, followed by a phoneme assembly to reconstruct word phonology, involving the left inferior frontal cortex. To allow the identification and comprehension of known words, the inferior frontal cortex then interacts with the semantic system via the left angular gyrus. As such, the left angular gyrus is likely to host phonological and semantic representations and serves as a bidirectional interface between the networks involved in language perception and word comprehension.

Lack of structural brain alterations associated with insomnia: findings from the <scp>ENIGMA‐Sleep</scp> Working Group

Abstract: Existing neuroimaging studies have reported divergent structural alterations in insomnia disorder (ID). In the present study, we performed a large-scale coordinated meta-analysis by pooling structural brain measures from 1085 subjects (mean [SD] age 50.5 [13.9] years, 50.2% female, 17.4% with insomnia) across three international Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA)-Sleep cohorts. Two sites recruited patients with ID/controls: Freiburg (University of Freiburg Medical Center, Freiburg, Germany) 42/43 and KUMS (Kermanshah University of Medical Sciences, Kermanshah, Iran) 42/49, while the Study of Health in Pomerania (SHIP-Trend, University Medicine Greifswald, Greifswald, Germany) recruited population-based individuals with/without insomnia symptoms 75/662. The influence of insomnia on magnetic resonance imaging-based brain morphometry using an insomnia brain score was then assessed. Within each cohort, we used an ordinary least-squares linear regression to investigate the link between the individual regional cortical and subcortical volumes and the presence of insomnia symptoms. Then, we performed a fixed-effects meta-analysis across cohorts based on the first-level results. For the insomnia brain score, weighted logistic ridge regression was performed on one sample (Freiburg), which separated patients with ID from controls to train a model based on the segmentation measurements. Afterward, the insomnia brain scores were validated using the other two samples. The model was used to predict the log-odds of the subjects with insomnia given individual insomnia-related brain atrophy. After adjusting for multiple comparisons, we did not detect any significant associations between insomnia symptoms and cortical or subcortical volumes, nor could we identify a global insomnia-related brain atrophy pattern. Thus, we observed inconsistent brain morphology differences between individuals with and without insomnia across three independent cohorts. Further large-scale cross-sectional/longitudinal studies using both structural and functional neuroimaging are warranted to decipher the neurobiology of insomnia.

ExpressInHost: A Codon Tuning Tool for the Expression of Recombinant Proteins in Host Microorganisms

Abstract: ExpressInHost (https://gitlab.com/a.raguin/expressinhost) is a GTK/C++ based user friendly graphical interface that allows tuning the codon sequence of an mRNA for recombinant protein expression in a host microorganism. Heterologous gene expression is widely implemented in biotechnology companies and academic research laboratories. However, expression of recombinant proteins can be challenging. On the one hand, maximising translation speed is important, especially in scalable production processes relevant to biotechnology companies, but on the other hand, solubility problems often arise as a consequence, since translation ‘pauses’ might be key to allow the nascent polypeptide chain to fold appropriately. To address this challenge, we have developed a software that offers three distinct modes to tune codon sequences using the genetic code redundancy. The tuning strategies implemented take into account the specific tRNA resources of the host and that of the native organism. They balance rapid translation and native speed mimicking, which might be important to allow proper protein folding, thereby avoiding protein solubility problems.

Moralische Empfindungen und Intuitionen

Abstract: DieIntuition, moralische PerspektiveGefühl (s. a. Affekt) derGefühl (s. a. Affekt)moralisches Moral (der moral point of view) ist keine der Welt rein betrachtend, beschreibend oder messend gegenüberstehende Perspektive, sondern eine wertende Einstellung mit gefühlshaften Elementen. Dies zeigt sich sowohl in den Sprachformen, mit denen wir moralische Einstellungen ausdrücken, als auch in den inneren Zuständen, die auf der Seite des moralisch Urteilenden und Bewertenden das moralische Urteil begleiten. Typische moralische Urteile enthalten neben beschreibenden Anteilen wertende Anteile, in ihnen drücken sich bestimmte Pro- und Kontra-Einstellungen aus.

What controls carbon sequestration in plants under which conditions?

Abstract: Photosynthetic organisms use photosynthesis to harvest sunlight and convert the solar energy into chemical energy, which is then used to reduce atmospheric carbon dioxide into organic molecules. This process forms the basis of all life on Earth, and stands at the beginning of the food chain which feeds the world population. Not surprisingly, many research efforts are currently ongoing aiming at improving growth and product yield of photosynthetic organisms, and several of these activities directly target the photosynthetic pathways. Metabolic Control Analysis (MCA) shows that, in general, the control over a metabolic flux, such as carbon fixation, is distributed among several steps and highly dependent on the external conditions. Therefore, the concept of a single 'rate-limiting' step is hardly ever applicable, and as a consequence, any strategy relying on improving a single molecular process in a complex metabolic system is bound to fail to yield the expected results. In photosynthesis, reports on which processes exert the highest control over carbon fixation are contradictory. This refers to both the photosynthetic 'light' reactions harvesting photons and the 'dark' reactions of the Calvin-Benson-Bassham Cycle (CBB cycle). Here, we employ a recently developed mathematical model, which describes photosynthesis as an interacting supply-demand system, to systematically study how external conditions affect the control over carbon fixation fluxes.

Evolution of Making Clinical Predictions in Neurosurgery

Abstract: Prediction of clinical outcomes is an essential task for every physician. Physicians may base their clinical prediction of an individual patient on their intuition and on scientific material such as studies presenting population risks and studies reporting on risk factors (prognostic factors). A relatively new and more informative approach for making clinical predictions relies on the use of statistical models that simultaneously consider multiple predictors that provide an estimate of the patient’s absolute risk of an outcome. There is a growing body of literature in the neurosurgical field reporting on clinical prediction models. These tools have high potential in supporting (not replacing) neurosurgeons with their prediction of a patient’s outcome. If used sensibly, these tools pave the way for more informed decision-making with or for individual patients. Patients and their significant others want to know their risk of the anticipated outcome, how it is derived, and the uncertainty associated with it. Learning from these prediction models and communicating the output to others has become an increasingly important skill neurosurgeons have to master. This article describes the evolution of making clinical predictions in neurosurgery, synopsizes key phases for the generation of a useful clinical prediction model, and addresses some considerations when deploying and communicating the results of a prediction model. The paper is illustrated with multiple examples from the neurosurgical literature, including predicting arachnoid cyst rupture, predicting rebleeding in patients suffering from aneurysmal subarachnoid hemorrhage, and predicting survival in glioblastoma patients.

Open Corpus Linguistics – or How to overcome common problems in dealing with corpus data by adopting open research practices

Abstract: In recent years, many researchers have called attention to the fact that many research results cannot be replicated – a phenomenon that has been called replication crisis. The replication crisis in linguistics is highly relevant to corpus-based research: Many corpus studies are not directly replicable as the data on which they are based are not readily available. Especially in English linguistics, the full versions of many widely used corpora are still behind paywalls, which means that they are not accessible to parts of the global research community, and even when parts of the data are freely accessible, this presents problems for state-of-the-art methods of data analysis. In this paper, I discuss the challenges that have led to this situation, and I address some possible solutions. In particular, I argue for using smaller but openly available corpora whenever possible, and for adopting open research practices as far as possible even when using commercial corpora.

Influence of Storage Conditions on Decellularized Porcine Conjunctiva

Abstract: Porcine decellularized conjunctiva (PDC) represents a promising alternative source for conjunctival reconstruction. Methods of its re-epithelialization in vitro with primary human conjunctival epithelial cells (HCEC) have already been established. However, a long-term storage method is required for a simplified clinical use of PDC. This study investigates the influence of several storage variants on PDC. PDC were stored in (1) phosphate-buffered saline solution (PBS) at 4 °C, (2) in glycerol-containing epithelial cell medium (EM/gly) at -80 °C and (3) in dimethyl sulfoxide-containing epithelial cell medium (EM/DMSO) at -196 °C in liquid nitrogen for two and six months, respectively. Fresh PDC served as control. Histological structure, biomechanical parameters, the content of collagen and elastin and the potential of re-epithelialization with primary HCEC under cultivation for 14 days were compared (n = 4-10). In all groups, PDC showed a well-preserved extracellular matrix without structural disruptions and with comparable fiber density (p ≥ 0.74). Collagen and elastin content were not significantly different between the groups (p ≥ 0.18; p ≥ 0.13, respectively). With the exception of the significantly reduced tensile strength of PDC after storage at -196 °C in EM/DMSO for six months (0.46 ± 0.21 MPa, p = 0.02), no differences were seen regarding the elastic modulus, tensile strength and extensibility compared to control (0.87 ± 0.25 MPa; p ≥ 0.06). The mean values of the epithelialized PDC surface ranged from 51.9 ± 8.8% (-196 °C) to 78.3 ± 4.4% (-80 °C) and did not differ significantly (p ≥ 0.35). In conclusion, all examined storage methods were suitable for storing PDC for at least six months. All PDC were able to re-epithelialize, which rules out cytotoxic influences of the storage conditions and suggests preserved biocompatibility for in vivo application.

Controlling weighted voting games by deleting or adding players with or without changing the quota

Abstract: Abstract Weighted voting games are a well-studied class of succinct simple games that can be used to model collective decision-making in, e.g., legislative bodies such as parliaments and shareholder voting. Power indices [1–4] are used to measure the influence of players in weighted voting games. In such games, it has been studied how a distinguished player’s power can be changed, e.g., by merging or splitting players (the latter is a.k.a. false-name manipulation) [5, 6], by changing the quota [7], or via structural control by adding or deleting players [8]. We continue the work on the structural control initiated by Rey and Rothe [8] by solving some of their open problems. In addition, we also modify their model to a more realistic setting in which the quota is indirectly changed during the addition or deletion of players (in a different sense than that of Zuckerman et al. [7] who manipulate the quota directly without changing the set of players), and we study the corresponding problems in terms of their computational complexity.