Biology subjects

Prati, D.

Publications and source records attributed to Prati, D..

9 recordsLinked to original sources

bioRxiv2025

Engineered Living Materials for Bioproduction Downstream Processing

De novo engineered living materials (ELMs) are cellular systems that self-assemble into macroscopic structures through genetically encoded interactions, offering a route to programmable materials grown directly from living cells. Despite their promise, the molecular design principles that enable scalable self-assembly in de novo ELMs remain poorly understood. Here, we engineer Escherichia coli to display elastin-like polypeptides (ELPs) on the outer membrane, transforming single cells into self-assembling living materials through weak intermolecular interactions. By tuning the polarity of ELP sequences, we generate assemblies spanning micrometer- to centimeter-length scales that sediment within a few hours while preserving cellular metabolic activity. We demonstrate the portability of this platform across genetic backgrounds and inducible expression systems, and deploy it in an ethanologenic E. coli strain as a proof of principle. In small-scale fermentation settings, ELP-based ELMs enable controllable flocculation, reduce filtration time by more than threefold, and maintain ethanol production performance comparable to that of the parental strain. Together, this work establishes ELP surface display as a modular strategy for constructing de novo engineered living materials and defines initial genetic design rules linking molecular-scale interactions to emergent macroscopic organization.

synthetic biology↗

bioRxiv2025

Competing gene regulatory networks drive naive and memory B cell differentiation

Elucidating the gene regulatory networks (GRNs) that govern human B cell differentiation is essential for understanding immune responses to infection, vaccination and autoantigens. Here, we show that individual naive B cells can give rise to both plasma cells and germinal centre (GC) B cells. In contrast, memory B cells display a progressive increase in IRF4 activity over time, leading to PRDM1 induction and exclusive differentiation into plasma cells. Using CRISPR-based perturbations, we demonstrate that IRF4 is indispensable for both GC and plasma cell development. Notably, IRF4 promotes GC fate independently of PRDM1, as PRDM1 disruption did not impair GC differentiation. We also find that while the abundance of antibody mRNAs is clonally correlated, class switch recombination (CSR) occurs stochastically and is clonally independent. Together, these findings reveal distinct regulatory dynamics during naive and memory B cell activation and offer new insights into the GRNs underlying human B cell fate decisions.

immunology↗

bioRxiv2025

Experimental reduction of land use increases invertebrate abundance but not diversity in grasslands

Grasslands are diverse ecosystems that are increasingly threatened by intensive land use. Restoring grasslands by reducing land-use intensity may support insect abundance and diversity, helping to halt insect declines. To test for the effect of reduced land use on invertebrates, we studied an experiment (established 2020) at 45 sites across three regions of Germany. We hypothesized that reduced land use increases invertebrate abundance and diversity, with larger effects in less intensively used grasslands. Using suction sampling, invertebrates were quantitatively sampled in May 2021 and May 2023, with 2021 samples identified by DNA meta-barcoding. Reducing land use to a single late mowing increased invertebrate abundance by 41% after one year and 99% after three years. However, species richness, Shannon diversity, and Simpson diversity did not differ between treatments and controls. Finding more individuals in grasslands with reduced land use suggests that species already present benefit, rather than additional species being recruited from the surrounding area. The effect of land-use reduction on abundance was consistently influenced by land use in the surrounding matrix, with larger positive effect sizes at grasslands with lower mowing frequency but higher fertilization. In spite of these local differences in the magnitude of restoration effects, the consistent increase in invertebrate abundance suggests that reducing land-use intensity can enhance invertebrate populations with potential benefits for ecosystem functions. It will be important to study how outcomes of land-use reduction develop over time, as land-use reduction is likely more successful when implemented permanently.

ecology↗

bioRxiv2024

Impact of land-use intensity, productivity, and aboveground richness on seed rain in temperate grasslands

O_LISeed rain, the amount of seeds reaching an area via primary or secondary dispersal, affects the regeneration of plant communities and shapes the trajectory of future community composition. In agricultural grasslands, the composition and density in seed rain are mainly driven by land use, but drivers of seed rain quality and quantity along land-use gradients are poorly understood. We studied the effects of land-use intensity (LUI), its components (i.e. fertilization, mowing, and grazing), productivity, and aboveground vegetation composition and richness on seed rain. C_LIO_LIWe collected the seed rain over a five-month period in 142 grasslands and identified emerging seedlings. Grass seedlings dominated seed rain most likely due to their high abundance in vegetation and intense and early seed set. Only ten species accounted for approximately 80 % of seedlings, with grasses such as Lolium perenne and Alopecurus pratensis being most abundant. Forbs such as Cerastium holosteoides and Veronica arvensis were abundant in seed rain despite lower cover, probably due to early and prolonged flowering and high seed production. C_LIO_LISeed rain of grasses and forbs reacted differently to LUI and vegetation richness, LUI effects on grass seed rain mainly determined total seed density. Seed rain richness first increased with LUI, but decreased at higher LUI levels. Consequently, seed rain richness consistently increased with vegetation richness. This is reflected by a decrease in the abundance of stress strategists and an increase in ruderals in seed rain with increasing LUI and decreasing vegetation richness. C_LIO_LIAmong LUI components, fertilization intensity most strongly affected seed rain density and composition, with negative effects at intermediate fertilization intensities. Mowing once a year increased seed rain density, whereas it decreased at higher mowing frequencies. Grazing intensity reduced overall seed density and richness by reducing grass seed density, while forb seed density remained unaffected. C_LI Synthesis: Land-use intensity and aboveground productivity significantly influence the species composition and seed densities in the seed rain of temperate agricultural grasslands. Higher land-use intensity and productivity increased seed production but reduced taxonomic and functional diversity in seed rain and may negatively impact ecosystem stability and resilience.

ecology↗

bioRxiv2024

Regulatory T-cells in multiple sclerosis are activated by Epstein-Barr Virus and produce IL-10 in the central nervous system

Regulatory T-cells (Tregs) maintain immune homeostasis, but antigens activating adaptive Tregs in human pathologies are ill-defined. EOMES+type-1 regulatory (Tr1)-like T-cells had a dysregulated homeostasis in multiple sclerosis (MS), which was related to their activation in the central nervous system (CNS). EOMES+Tr1-like cells were enriched and clonally expanded in patients cerebrospinal fluid (CSF) and were the major IL-10-producing T-cell subset in the CNS. Regulatory T-cells from PwMS produced IL-10 and IFN-{gamma} with antigens derived from Epstein-Barr Virus (EBV), but not from myelin. EOMES+Tr1-like cells responded selectively to the latency-associated antigen EBNA1, whereas FOXP3+Tregs and Th1-cells responded also to lytic EBV antigens. EBNA1-specific EOMES+Tr1-like cells were present in patients carrying the HLA-DRB1*15:01 risk allele, were associated with anti-EBNA1 IgG and disappeared upon therapeutic B-cell depletion. IL-10+EOMES+Tr1-like were present in MS brain lesions, and some were in the vicinity of EBV-infected B-cells and CD8+T-cells. Notably, EOMES+Tr1-like cells suppressed CD8+T-cell activation by EBV-infected B-cells. We propose that the insufficient protective functions of Tregs in MS are due to their aberrant anti-viral specificities that promote immune escape of a disease-associated virus.

immunology↗

bioRxiv2022

Loss of species richness with land use intensity is explained by a reduction in niche differences.

Increases in land use intensity (LUI) reduce species richness. However, we have a poor understanding of how underlying coexistence mechanisms are altered by land use and whether diversity loss occurs due to changes in plant-plant interactions (competition and facilitation) or in species intrinsic growth rates. We expect that LUI could reduce stabilizing niche differences and the indirect interactions that promote coexistence (e.g., intransitivity), while increasing competitive inequalities between species. To test the importance of these different processes, we use 8-yr time series from 150 grasslands differing in LUI to evaluate the role of direct and indirect interactions in promoting coexistence between 50 plant species. We show that LUI reduces the number of coexisting species mostly by causing a non-linear reduction in niche differences, rather than by enhancing competitive inequalities. However, surprisingly, niche differences remained important in stabilizing coexistence between those species remaining at high LUI. Indirect interactions were generally less important than direct ones, and played a moderate role in promoting coexistence in smaller assemblages of species at intermediate LUI. Our models could accurately reproduce the decline in diversity seen with LUI, indicating that our time series approach captures the important interactions between species. By analyzing land use effects through recent advances in structural stability applied to community ecology we provide a more mechanistic understanding of its effects. Our results highlight the importance of identifying the niche differences that are lost with increasing LUI, to better predict and manage effects of land use on biodiversity. Significant statementHuman land use is a major threat to grassland biodiversity. Grasslands with high rates of fertilization, grazing and mowing, contain many fewer plant species. Knowing the underlying causes is necessary for a better management of biodiversity. Here we apply ecological theory to spatiotemporal data on changes in plant abundance in managed grasslands in central Europe. We show that the observed decline in diversity can be explained by how interactions among plant species change with increases in land use intensity. In particular, intensive land use removes the stabilizing effect of self-limiting processes that buffer species against extinction as well as limit competitive dominance. Therefore, actions to promote these stabilizing dynamics among interacting species seem key to restore plant diversity.

ecology↗

bioRxiv2020

Landscape management for grassland multifunctionality

Land-use intensification has contrasting effects on different ecosystem services, often leading to land-use conflicts. While multiple studies have demonstrated how landscape-scale strategies can minimise the trade-off between agricultural production and biodiversity conservation, little is known about which land-use strategies maximise the landscape-level supply of multiple ecosystem services (landscape multifunctionality), a common goal of stakeholder communities. We combine comprehensive data collected from 150 German grassland sites with a simulation approach to identify landscape compositions, with differing proportions of low-, medium-, and high-intensity grasslands, that minimise trade-offs between the six main grassland ecosystem services prioritised by local stakeholders: biodiversity conservation, aesthetic value, productivity, carbon storage, foraging, and regional identity. Results are made accessible through an online tool that provides information on which compositions best meet any combination of user-defined priorities (https://neyret.shinyapps.io/landscape_composition_for_multifunctionality/). Results show that an optimal landscape composition can be identified for any pattern of ecosystem service priorities. However, multifunctionality was similar and low for all landscape compositions in cases where there are strong trade-offs between services (e.g. aesthetic value and fodder production), where many services were prioritised, and where drivers other than land use played an important role. We also found that if moderate service levels are deemed acceptable, then strategies in which both high and low intensity grasslands are present can deliver landscape multifunctionality. The tool presented can aid informed decision-making by predicting the impact of future changes in landscape composition, and by allowing for the relative roles of stakeholder priorities and biophysical trade-offs to be understood by scientists and practitioners alike. HighlightsO_LIAn online tool identifies optimal landscape compositions for desired ecosystem services C_LIO_LIWhen the desired services are synergic, the optimum is their common best landscape composition C_LIO_LIWhen the desired services trade-off, a mix of grassland intensity is most multifunctional C_LIO_LISuch tools could support decision-making processes and aid conflict resolution C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/208199v5_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@3273f6org.highwire.dtl.DTLVardef@5b3a5aorg.highwire.dtl.DTLVardef@153f526org.highwire.dtl.DTLVardef@103cbea_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2019

Context dependency of biotic interactions and its relation to plant rarity

AimBiotic interactions can determine rarity and commonness of species, however evidence that rare and common species respond differently to biotic stress is scarce. This is because biotic interactions are notoriously context-dependent and traits leading to success in one habitat might be costly or unimportant in another. We aim to identify plant characteristics that are related to biotic interactions and may drive patterns of rarity and commonness, taking environmental context into account.\n\nLocationSwitzerland\n\nMethodsIn a multi-species experiment, we compared the response to biotic interactions of 19 rare and 21 widespread congeneric plant species in Switzerland, while also accounting for variation in environmental conditions of the species origin.\n\nResultsOur results restrict the long-standing hypothesis that widespread species are superior competitors to rare species to only those species originating from resource rich habitats, in which competition is usually strong. Tolerance to herbivory and ambient herbivore damage on the other hand, did not differ between widespread and rare species. In accordance to the resource-availability hypothesis, widespread species from resource rich habitats where more damaged by herbivores (less defended) than widespread species from resource poor habitats - such a growth-defense tradeoff was lacking in rare species. This indicates that the evolutionary important tradeoff between traits increasing competitive-ability and defence is present in widespread species but may have been lost in rare species.\n\nMain conclusionsOur results indicate that biotic interactions, above all competition, might indeed set range limits, and underlines the importance of including context-dependency in studies comparing traits of common and rare or invasive and non-invasive species.

ecology↗

bioRxiv2019

The results of biodiversity-ecosystem functioning experiments are realistic

A large body of research shows that biodiversity loss can reduce ecosystem functioning, thus providing support for the conservation of biological diversity1-4. Much of the evidence for this relationship is drawn from biodiversity-ecosystem functioning experiments (hereafter: biodiversity experiments), in which biodiversity loss is simulated by randomly assembling communities of varying species diversity, and ecosystem functions are measured5-9. This random assembly has led some ecologists to question the relevance of biodiversity experiments to real-world ecosystems, where community assembly may often be non-random and influenced by external drivers, such as climate or land-use intensification10-18. Despite these repeated criticisms, there has been no comprehensive, quantitative assessment of how experimental and real-world plant communities really differ, and whether these differences invalidate the experimental results. Here, we compare data from two of the largest and longest-running grassland biodiversity experiments globally (Jena Experiment, Germany; BioDIV, USA) to related real-world grassland plant communities in terms of their taxonomic, functional, and phylogenetic diversity and functional-trait composition. We found that plant communities of biodiversity experiments have greater variance in these compositional features than their real-world counterparts, covering almost all of the variation of the real-world communities (82-96%) while also containing community types that are not currently observed in the real world. We then re-analysed a subset of experimental data that included only ecologically-realistic communities, i.e. those comparable to real-world communities. For ten out of twelve biodiversity-ecosystem functioning relationships, biodiversity effects did not differ significantly between the full dataset of biodiversity experiments and the ecologically-realistic subset of experimental communities. This demonstrates that the results of biodiversity experiments are largely insensitive to the inclusion/exclusion of unrealistic communities. By bridging the gap between experimental and real-world studies, these results demonstrate the validity of inferences from biodiversity experiments, a key step in translating their results into specific recommendations for real-world biodiversity management.

ecology↗