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The simulation experiment description markup language (SED-ML): language specification for level 1 version 5
No full textModern biological research is increasingly informed by computational simulation experiments, which necessitate the development of methods for annotating, archiving, sharing, and reproducing the conducted experiments. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. Level 1 Version 5 of SED-ML expands the ability of modelers to define simulations in SED-ML using the Kinetic Simulation Algorithm Onotoloy (KiSAO). While it was possible in Version 4 to define a simulation entirely using KiSAO, Version 5 now allows users to define tasks, model changes, ranges, and outputs using the ontology as well. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including various languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, and many simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/ .The Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the LiverNational Science FoundationGerman Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerFNational Institute of General Medical SciencesNational Institute for Biomedical Imaging and BioengineeringFederal Ministry of Education and Research (BMBF, Germany) within the research network de.NBINational Institute of Health SciencesNational Institute for Biomedical Imaging and BioengineeringPeer Reviewe
Deliberately ignoring inequality to avoid rejecting unfair offers
No full textWhy do people punish experienced unfairness if it induces costs for both the punisher and punished person(s) without any direct material benefits for the punisher? Economic theories of fairness propose that punishers experience disutility from disadvantageous inequality and punish in order to establish equality in outcomes. We tested these theories in a modified Ultimatum Game ( N = 1370) by examining whether people avoid the urge to reject unfair offers, and thereby punish the proposer, by deliberately blinding themselves to unfairness. We found that 53% of participants deliberately ignored whether they had received an unfair offer. Among these participants, only 6% of offers were rejected. As expected, participants who actively sought information rejected significantly more unfair offers (39%). Averaging these rejection rates to 21%, no significant difference to the rejection rate by participants who were directly informed about unfairness was found, contrary to our hypothesis. We interpret these findings as evidence for sorting behavior: People who punish experienced unfairness seek information about it, while those who do not punish deliberately ignore it.Peer Reviewe
Combining biotelemetry and genetics provides complementary insights relevant to the management and conservation of a freshwater predator (Esox lucius) living in brackish lagoons
No full textTo inform the management of wild fish populations, it is equally important to understand both the ecological connectivity of habitat patches, apparent at annual and seasonal scales, and the genetic connectivity, emerging at evolutionary scales across generations. Ecological connectivity indicates the potential for rapid recolonization upon local depletion, while genetic connectivity informs about the conservation needs related to the evolution of subpopulations and ecotypes in metapopulations. We combined acoustic biotelemetry and pooled-genome sequencing to study a northern pike ( Esox lucius ) population as a model of a freshwater piscivore that inhabits a network of shallow brackish lagoons in the southern Baltic Sea. We found limited ecological connectivity among genetically similar subpopulations of pike, suggesting a metapopulation structure characterized by discrete local subpopulations with infrequent migrations between them. Connectivity of different lagoons increased during spawning, suggesting directed spawning migrations to either freshwater rivers or low salinity patches in connected lake-like bays. Spawning site fidelity to either brackish or freshwater spawning sites was observed, further contributing to the reproductive isolation of certain subpopulations. The genetic population structure aligned with salinity gradients and geographical distance and was significant between pairs of rivers draining into the lagoon network, but it was unrelated to ecological connectivity. The results collectively suggest that local subpopulations may not rapidly replenish upon local depletion and that even weak connectivity among subpopulations was sufficient to maintain genetic homogeneity across lagoons with similar salinity levels. Effective management and conservation of species forming metapopulations, such as the coastal northern pike studied here, necessitate localized approaches that adapt fishing mortality to local abundance and promote access to specific habitats, especially rivers, during spawning to conserve the entire genetic biodiversity and foster resilience of the metapopulation.Peer Reviewe
A phosphate starvation induced small RNA promotes Bacillus biofilm formation
No full textCurrently, almost all known regulators involved in bacterial phosphorus metabolism are proteins. In this study, we identified a conserved new small regulatory RNA (sRNA), named PhoS, encoded in the 3’ untranslated region (UTR) of the phoPR genes in Bacillus velezensis and B. subtilis . Expression of phoS is strongly induced upon phosphorus scarcity and stimulated by the transcription factor PhoP. Conversely, PhoS positively regulates PhoP translation by binding to the ribosome binding site (RBS) of phoP mRNA. PhoS can promote Bacillus biofilm formation through, at least in part, enhancing the expression of the matrix-related genes, such as the eps genes and the tapA-sipW-tasA operon. The positive regulation of phoP expression by PhoS contributes to the promoting effect of PhoS on biofilm formation. sRNAs regulating biofilm formation have rarely been reported in gram-positive Bacillus species. Here we highlight the significance of sRNAs involved in two important biological processes: phosphate metabolism and biofilm formation.National Natural Science Foundation of China (National Science Foundation of China)https://doi.org/10.13039/501100001809National Key R&D Program of China (2023YFD1401304, 2021YFD1400300)Peer Reviewe
The personality of coaches: a quantitative research of the big five personality traits of coaches
No full textIn dieser empirischen Studie wird untersucht, ob Coaches eine andere Persönlichkeitsausprägung aufweisen als die Allgemeinbevölkerung. Hierzu wurden Daten von 559 deutschsprachigen Coaches mit Hilfe eines Persönlichkeitsfragebogen im Rahmen der Coachingumfrage Deutschland 2022 erhoben und mit vorhandenen Referenzdaten aus der Allgemeinbevölkerung verglichen. Die Datenerhebung zur Persönlichkeit erfolgte mit der deutschen Version des Big Five Inventory 2 (BFI-2). Die Ergebnisse zeigen, dass die untersuchten Coaches signifikant extravertierter, verträglicher, gewissenhafter, offener und weniger emotional labil (neurotizistisch) als die Allgemeinbevölkerung sind.This empirical study investigates whether coaches have a different personality trait to the general population. To this end, data from 559 German-speaking coaches was collected using a personality questionnaire as part of the Coaching Survey Germany 2022 and compared with existing reference data from the general population. Personality data was collected using the German version of the Big Five Inventory 2 (BFI-2). The results show that the surveyed coaches are significantly more extraverted, more agreeable, more conscientious, more open, and less emotionally unstable (neuroticism) than the general population.Open Access funding enabled and organized by Projekt DEAL.Humboldt-Universität zu Berlin (1034)Peer Reviewe
Nonlinear vibrational spectrometer for bioapplications featuring narrowband 1-μm pulses and a recycled OPA pump beam
No full text© 2024 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement (https://opg.optica.org/content/library/portal/item/license_v2#VOR-OA). Readers may use, reuse, and build upon the article, or use it for text or data mining without asking prior permission from the publisher or the Author(s), as long as the purpose is non-commercial and appropriate attribution is maintained.Moving the detection wavelength in vibrational sum-frequency generation (VSFG) spectroscopy to the near-infrared (> 700 nm) is crucial to avoid autofluorescence and electronic resonance effects distorting the molecular phase response or triggering unwanted chemical and photophysical reactions. Here, we employ an ultra-narrow bandpass interference filter on Yb laser pulses to generate an upconversion beam near 1.03 μm at a spectral resolution of 5 cm−1. We demonstrate that the beam rejected by the filter can be utilized for driving a supercontinuum-seeded near-infrared optical parametric amplifier, boosting the seed energy for a broadband LiGaS2-based mid-infrared amplifier. Through the example of a chromoprotein, we show that utilizing the scheme can extend the range of interfacial molecular systems that can be studied using VSFG spectroscopy, even in the case of high repetition rate Yb pump lasers with limited pulse energy. The scheme can also be utilized in other types of vibrational spectroscopie that derive their spectral resolution from bandpass-filtering of femtosecond near-infrared laser pulses, such as stimulated Raman scattering (SRS) and coherent anti-Stokes Raman scattering (CARS) spectroscopy.Peer Reviewe
Biotic interactions between the human pathogen Legionella pneumophila and nematode grazers in cooling tower biofilms
No full textBiofilms in cooling towers represent a common habitat for the human pathogen Legionella pneumophila. Within the biofilm consortium, frequent interactions with protozoa, i.e. amoebae and ciliates, were reported, while nematodes have only recently been considered as potential environmental reservoir for the pathogenic bacteria. This study is the first approach to investigate the biotic interactions between L. pneumophila and bacterial-feeding nematodes in a semi-natural biofilm model. The species were Diploscapter coronatus, Diploscapter pachys, Plectus similis and Plectus sp., which all co-occur with L. pneumophila in the environment. Biofilms derived from cooling towers were either inoculated with mCherry-labeled L. pneumophila solely or in combination with GFP-labeled Escherichia coli. All experiments were conducted in single-species set-ups and multi-species (D. coronatus and P. similis) set-ups, to account for interspecific competition. Bacterial ingestion was assessed after 24 and 96 h as fluorescence patterns in the digestive tract of the nematodes using confocal laser scanning microscopy. L. pneumophila cells were ingested by all nematode species, with D. coronatus having the highest pathogen load. The fluorescence intensity (i.e. bacterial load) varied between compartments within the digestive tract and was independent of incubation time. Bacterial cells accumulated mostly around the cardia and in the intestine, while less cells were found within stoma and pharynx. Interspecific competition changed the pattern, i.e. with incubation of D. coronatus and P. similis in the same biofilm a significantly higher pathogen load occurred in the intestine of D. coronatus than P. similis after 24 h and 96 h. Remarkably, when given a choice between L. pneumophila and E. coli, P. similis was the only nematode species containing both bacteria after incubation for 24 h. None of the other nematode species contained E. coli after 24 h and 96 h incubation, while L. pneumophila was present. This study thus provides the first evidence, that under environmental conditions L. pneumophila is a frequent diet of bacterial-feeding nematodes, highlighting their potential as pathogen vectors or even host in cooling tower habitats.Peer Reviewe
Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network
No full textB cell receptor (BCR) signaling is required for the survival and maturation of B cells and is deregulated in B cell lymphomas. While proximal BCR signaling is well studied, little is known about the crosstalk of downstream effector pathways, and a comprehensive quantitative network analysis of BCR signaling is missing. Here, we semi-quantitatively modelled BCR signaling in Burkitt lymphoma (BL) cells using systematically perturbed phosphorylation data of BL-2 and BL-41 cells. The models unveiled feedback and crosstalk structures in the BCR signaling network, including a negative crosstalk from p38 to MEK/ERK. The relevance of the crosstalk was verified for BCR and CD40 signaling in different BL cells and confirmed by global phosphoproteomics on ERK itself and known ERK target sites. Compared to the starting network, the trained network for BL-2 cells was better transferable to BL-41 cells. Moreover, the BL-2 network was also suited to model BCR signaling in Diffuse large B cell lymphoma cells lines with aberrant BCR signaling (HBL-1, OCI-LY3), indicating that BCR aberration does not cause a major downstream rewiring.Author summary: B cell receptors bind specific antigens, and upon binding, they activate a signal transduction network which ultimately primes the cells for proliferation and affinity maturation. B-cell receptor signaling is often altered in B-cell lymphoma, leading to altered or chronic activation of the network. In this study we compared the signal transduction network downstream of acute and aberrant B cell receptor activity in cell lines originating from Burkitt and diffuse large B-cell lymphoma, respectively. By applying kinase inhibitors, we measured phosphorylation state changes in the network nodes. Mathematical modeling revealed a 16-node core network conserved in cells with acute and abberant B cell receptor signaling. In the network we detected hitherto undescribed crosstalks and feedbacks, structures known to confer treatment robustness. We elucidated and verified a negative crosstalk between the mitogen-activated protein kinases (MAPK) p38 and ERK. We further discovered that the negative feedback from ERK to its upstream kinase RAF, which in solid tumors neutralizes treatments targeting ERK or MEK, is also present in B cells. Altogether these findings may inform future treatment strategies targeting overactive B cell receptor or help to explain treatment resistance.Peer Reviewe
A One Health perspective on recreational fisheries
No full textRecreational fisheries involve an intimate connection between people, individual fish, and the environment. Recreational fishers and their health crucially depend on healthy fish and ecosystems. Similarly, fish and ecosystems can be impacted by the activities of people including recreational fishers. Thus, amplified by the global interest in recreational fishing, we posit that recreational fishing is particularly suited as an empirical system to explore a One Health perspective, with a goal of creating pathways to better manage such socio-ecological systems for the benefit of people, fish, and the environment. Although zoonoses are uncommon in fishes, fish can carry pathogens, biotoxins, or contaminants that are harmful to people. When captured and released, fish can experience stress and injuries that may promote pathogen development. Similarly, when humans contribute to environmental degradation, not only are fish impacted but so are the humans that depend on them for nutrition, livelihoods, culture, and well-being. Failure to embrace the One Health perspective for recreational fisheries has the potential to negatively impact the health of fish, fisheries, people, society, and the aquatic environment—especially important since these complex social–ecological systems are undergoing rapid change.Peer Reviewe
Porous aluminum decorated with rhodium nanoparticles: preparation and use as a platform for UV SERS†
No full textCurrently, there is a high interest in novel plasmonic platforms and materials able to extend their applicability into the ultraviolet (UV) region of the electromagnetic spectrum. In the UV it is possible to explore the spectral properties of biomolecules that have only a small cross-section in the visible spectral range. However, most plasmonic metals have their resonances at wavelengths >350 nm. Aluminum and rhodium are two exceptions and therefore interesting candidate materials for UV plasmonics. In this work we developed a simple and low-cost preparation of functional substrates based on nanoporous aluminum decorated with rhodium nanoparticles. We demonstrate that these functionalized nanoporous metal films can be exploited as plasmonic materials for enhanced UV Raman spectroscopy.Peer Reviewe