T Cells Integrate Local and Global Cues to Discriminate between Structurally Similar Antigens

International audienceT lymphocytes' ability to discriminate between structurally related antigens has been attributed to the unique signaling properties of the T cell receptor. However, recent studies have suggested that the output of this discrimination process is conditioned by environmental cues. Here, we demonstrate how the IL-2 cytokine, collectively generated by strongly activated T cell clones, can induce weaker T cell clones to proliferate. We identify the PI3K pathway as being critical for integrating the antigen and cytokine responses and for controlling cell-cycle entry. We build a hybrid stochastic/deterministic computational model that accounts for such signal synergism and demonstrates quantitatively how T cells tune their cell-cycle entry according to environmental cytokine cues. Our findings indicate that antigen discrimination by T cells is not solely an intrinsic cellular property but rather a product of integration of multiple cues, including local cues such as antigen quality and quantity, to global ones like the extracellular concentration of inflammatory cytokines

What is the benefit of ceilometers for aerosol remote sensing? An answer from EARLINET

With the establishment of ceilometer networks by national weather services, a discussion commenced to which extent these simple backscatter lidars can be used for aerosol research. Though primarily designed for the detection of clouds it was shown that at least observations of the vertical structure of the boundary layer might be possible. However, an assessment of the potential of ceilometers for the quantitative retrieval of aerosol properties is still missing. In this paper we discuss different retrieval methods to derive the aerosol backscatter coefficient beta(p),with special focus on the calibration of the ceilometers. Different options based on forward and backward integration methods are compared with respect to their accuracy and applicability. It is shown that advanced lidar systems such as those being operated in the framework of the European Aerosol Research Lidar Network (EARLINET) are excellent tools for the calibration, and thus beta(p) retrievals based on forward integration can readily be implemented and used for real-time applications. Furthermore, we discuss uncertainties introduced by incomplete overlap, the unknown lidar ratio, and water vapor absorption. The latter is relevant for the very large number of ceilometers operating in the spectral range around lambda = 905-910 nm. The accuracy of the retrieved beta(p) mainly depends on the accuracy of the calibration and the long-term stability of the ceilometer. Under favorable conditions, a relative error of beta(p) on the order of 10% seems feasible. In the case of water vapor absorption, corrections assuming a realistic water vapor distribution and laser spectrum are indispensable;otherwise errors on the order of 20% could occur. From case studies it is shown that ceilometers can be used for the reliable detection of elevated aerosol layers below 5 km, and can contribute to the validation of chemistry transport models, e. g.,the height of the boundary layer. However, the exploitation of ceilometer measurements is still in its infancy, so more studies are urgently needed to consolidate the present state of knowledge, which is based on a limited number of case studies

FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum

The MIPS Fusarium graminearum Genome Database (FGDB) was established as a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat, barley and maize. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The results of gene prediction tools were integrated with the help of comparative data on related species to result in a set of 13.718 annotated protein coding genes. This rigorous approach involved adding or modifying gene models and represents a coding sequence gold standard for the genus Fusarium. The gene loci improvements results in 2461 genes which either are new or have different structures compared to the Broad Institute assembly 3 gene set. Moreover the database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets. The resource is accessible on http://mips.gsf.de/genre/proj/FGDB/

Reporting quality of published reviews of commercial and publicly available mobile health apps (mHealth app reviews): A scoping review protocol

\ua9 Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY. Published by BMJ.Introduction Reviews of commercial and publicly available smartphone (mobile) health applications (mHealth app reviews) are being undertaken and published. However, there is variation in the conduct and reporting of mHealth app reviews, with no existing reporting guidelines. Building on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we aim to develop the Consensus for APP Review Reporting Items (CAPPRRI) guidance, to support the conduct and reporting of mHealth app reviews. This scoping review of published mHealth app reviews will explore their alignment, deviation, and modification to the PRISMA 2020 items for systematic reviews and identify a list of possible items to include in CAPPRRI. Method and analysis We are following the Joanna Briggs Institute approach and Arksey and O\u27Malley\u27s five-step process. Patient and public contributors, mHealth app review, digital health research and evidence synthesis experts, healthcare professionals and a specialist librarian gave feedback on the methods. We will search SCOPUS, CINAHL Plus, AMED, EMBASE, Medline, APA PsycINFO and the ACM Digital Library for articles reporting mHealth app reviews and use a two-step screening process to identify eligible articles. Information on whether the authors have reported, or how they have modified the PRISMA 2020 items in their reporting, will be extracted. Data extraction will also include the article characteristics, protocol and registration information, review question frameworks used, information about the search and screening process, how apps have been evaluated and evidence of stakeholder engagement. This will be analysed using a content synthesis approach and presented using descriptive statistics and summaries. This protocol is registered on OSF (https://osf.io/5ahjx). Ethics and dissemination Ethical approval is not required. The findings will be disseminated through peer-reviewed journal publications (shared on our project website and on the EQUATOR Network website where the CAPPRRI guidance has been registered as under development), conference presentations and blog and social media posts in lay language

Modelling human embryoid body cell adhesion to a combinatorial library of polymer surfaces

Designing materials to control biology is an intense focus of biomaterials and regenerative medicine research. Discovering and designing materials with appropriate biological compatibility or active control of cells and tissues is being increasingly undertaken using high throughput synthesis and assessment methods. We report a relatively simple but powerful machine-learning method of generating modelsthat link microscopic or molecular properties of polymers or other materials to their biological effects. We illustrate the potential of these methods by developing the first robust, predictive, quantitative, and purely computational models of adhesion of human embryonic stem cell embryoid bodies (hEB) to the surfaces of 496-member polymers

Morphology of supported polymer electrolyte ultra-thin films: a numerical study

Morphology of polymer electrolytes membranes (PEM), e.g., Nafion, inside PEM fuel cell catalyst layers has significant impact on the electrochemical activity and transport phenomena that determine cell performance. In those regions, Nafion can be found as an ultra-thin film, coating the catalyst and the catalyst support surfaces. The impact of the hydrophilic/hydrophobic character of these surfaces on the structural formation of the films has not been sufficiently explored yet. Here, we report about Molecular Dynamics simulation investigation of the substrate effects on the ionomer ultra-thin film morphology at different hydration levels. We use a mean-field-like model we introduced in previous publications for the interaction of the hydrated Nafion ionomer with a substrate, characterized by a tunable degree of hydrophilicity. We show that the affinity of the substrate with water plays a crucial role in the molecular rearrangement of the ionomer film, resulting in completely different morphologies. Detailed structural description in different regions of the film shows evidences of strongly heterogeneous behavior. A qualitative discussion of the implications of our observations on the PEMFC catalyst layer performance is finally proposed

Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. A Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wildtype. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this is the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation