Biology subjects

Blank, L.

Publications and source records attributed to Blank, L..

5 recordsLinked to original sources

bioRxiv2025

Comparative Analysis of Ecological and Germination Niches in Native and Invasive Populations of Amaranthus albus

Invasive species serve as natural experiments to study adaptive evolution over contemporary time scales, as their native and invasive populations are exposed to different climatic settings and hence may experience strong selection pressures. In the life cycle of plants, germination stands as a cornerstone; thus, when invasive plant species encounter new surroundings, it is primarily expected that their germination niche will adapt to align with the thermal characteristics of the environment. However, adaptive responses in germination traits, specifically in cardinal temperatures, have not been explored. The objective of this study is to compare the Amaranthus albus (tumble pigweed) germination thermal niche and ecological niche between its native and invaded ranges. Considering geographic areas and climatic conditions, populations of A. albus were gathered from both cold and warm habitats in its native range (US) and its invaded range (Israel), with populations being at least 20 km apart from each other. First, populations were grown under similar conditions in a common garden experiment until seed production. The progeny seeds produced were then subjected to a set of germination trials under gradually changing temperature regimes. Cardinal temperatures and thermal niches for each population were estimated and analyzed in relation to the local climatic conditions of their respective habitats. Finally, a germination window was calculated to characterize the germination of a population throughout the year within its habitat. The invaded range studied here represents a subset of the species native range, with the A. albus establishing in similar climatic surroundings. Similarly, the germination niche for the native range was wider than for the invaded range. Thermal differentiation is evident in both native and invaded ranges. Populations from colder habitats exhibit lower base temperatures than those from warmer ones. This association was more evident for native populations. The remarkable variability observed within the germination pattern completely disappeared in the germination window produced by those models, resulting in a similar pattern across the year for all populations. Our findings demonstrate the capability of species to adapt to new environmental conditions that may arise due to climatic changes. It emphasizes the role of cardinal temperatures, specifically the base temperature, as a potential adaptive characteristic.

ecology↗

bioRxiv2025

Murine model of antibiotic-associated S. aureus gastrointestinal infections (SAGII) and colonization

BackgroundStaphylococcus aureus is an opportunistic pathogen that can both colonize the gastrointestinal tract and cause antibiotic associated diarrhea. MethodsTo develop a robust murine model for S. aureus gastrointestinal infection (SAGII) and colonization, mice were (a) treated with varying antibiotic regimes prior to infection, (b) infected with either a methicillin-sensitive S. aureus (MSSA) or a methicillin-resistant S. aureus (MRSA) strain, (c) challenged with different bacterial inocula, (d) tested for sexual dimorphism of SAGII virulence, and (e) tested for macronutrient effects on SAGII onset and virulence. ResultsWe found that antibiotic-treated male mice (but not female mice) were highly susceptible to even low inoculums of both an MSSA and an MRSA strains. Interestingly, male mice challenged with an MSSA strain showed more severe and more prolonged SAGII symptomatology than animals challenged with an MRSA strain. We also showed that for male mice a high-carbohydrate diet and a high-fat diet led to asymptomatic intestinal colonization followed by delayed SAGII sign onset. In contrast, male mice fed a high-protein diet started developing mild SAGII signs early but did not develop severe SAGII until two weeks post-challenge. Furthermore, only the high-protein diet sensitized female mice to SAGII, but their symptomatology remained less severe than in male mice. ConclusionsWe developed a robust murine model for antibiotic-associated S. aureus gastrointestinal infection and colonization. This model shows both sexual dimorphism and macronutrient preference for SAGII severity. Diet manipulation can also be used to establish S. aureus colonization of the GI tract.

microbiology↗

bioRxiv2024

Quantifying Contributions from TopologicalCycles in the Brain Network towards Cognition

This study proposes a novel metric called Homological Vertex Importance Profile (H-VIP), utilizing topological data analysis tool persistent homology, to analyze human brain structural and functional connectomes. Persistent homology is a useful tool for identifying topological features such as cycles and cavities within a network. The salience of persistent homology lies in the fact that it offers a global view of the network as a whole. However, it falls short in precisely determining the relative relevance of the vertices of the network that contribute to these topological features. Our aim is to quantify the contribution of each individual vertex in the formation of homological cycles and provide insight into local connectivity. Our proposed H-VIP metric captures, quantifies, and compresses connectivity information from vertices even at multiple degrees of separation and projects back onto each vertex. Using this metric, we analyze two independent datasets: structural connectomes from the Human Connectome Project and functional connectomes from the Alzheimers Disease Neuroimaging Initiative. Our findings indicate a positive correlation between various cognitive measures and H-VIP, in both anatomical and functional brain networks. Our study also demonstrates that the connectivity in the frontal lobe has a higher correlation with cognitive performance compared to the whole brain network. Furthermore, the H-VIP provides us with a metric to easily locate, quantify, and visualize potentially impaired connectivity for each subject and may have applications in the context of personalized medicine for neurological diseases and disorders.

bioinformatics↗

bioRxiv2019

The metabolic response of Pseudomonas taiwanensis to NADH dehydrogenase deficiency

Obligate aerobic organisms rely on a functional electron transport chain for energy generation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions.\n\nWe here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the generated single or double knockout strains displayed none or only a marginal phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants including quantitative physiological experiments, transcript analysis, proteomics and enzyme activity assays revealed distinct responses to type II and type I dehydrogenase deletions. An overall high metabolic flexibility enables P. taiwanensis to cope with the introduced genetic perturbations and maintain stable phenotypes by rerouting of metabolic fluxes.\n\nThis metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, versatile redirecting of carbon fluxes upon genetic interventions can frustrate metabolic engineering efforts.\n\nImportanceWhile Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and consequently competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants of Pseudomonas taiwanensis VLB120 presented here, provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. The observed great metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse towards a host with controlled and efficient supply of redox cofactors for product synthesis.

physiology↗

bioRxiv2018

The role of land use types and water chemical properties in structuring the microbiome of a connected lakes system

Lakes and other freshwater bodies are intimately connected to the surrounding land, yet to what extent land-use affects the quality of freshwater and the microbial communities living in various freshwater environments is largely unknown. We address this question through an analysis of the land use surrounding 46 inter-connected lakes located within 7 different drainage basins in northern Germany, and the microbiomes of these lakes during early summer. Lake microbiome structure was not determined by the specific drainage basin or by basin size, and bacterial distribution did not seem to be limited by distance. Instead, land use within the drainage basin could predict, to some extent, NO2+NO3 concentrations in the water, which (together with temperature, chlorophyll a and total phosphorus) affected water microbiome structure. Land use directly surrounding the water bodies, however, had little observable effects on water quality or the microbiome. Several microbial lineages, including environmentally important Cyanobacteria and Verrucomicrobia, were differentially partitioned between the lakes. As the amount of available data on land use (e.g. from remote sensing) increases, identifying relationships between land use, aquatic microbial communities and their effect on water quality will be important to better manage freshwater resources worldwide, e.g. by systemically identifying water bodies prone to ecological changes or the presence of harmful organisms.

microbiology↗