Biology subjects

Schmid, B.

Publications and source records attributed to Schmid, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Genome-wide neighbor effects predict genotype pairs that reduce herbivory in mixed planting

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of both positive and negative effects of mixed planting on plant resistance, called associational resistance and susceptibility. We used genome-wide polymorphisms of the plant species Arabidopsis thaliana to identify genotype pairs that enhance associational resistance to herbivory. By quantifying neighbor interactions among 199 genotypes grown in a randomized block design, we predicted that 823 of the 19,701 candidate pairs could reduce herbivory through associational resistance. We planted such pairs with predicted associational resistance in mixtures and monocultures and found a significant reduction in herbivore damage in the mixtures. Our study highlights the potential application to assemble genotype mixtures with positive biodiversity effects.

ecology↗

bioRxiv2023

Plant diversity stabilizes soil temperature

Extreme weather events are occurring more frequently, and research has shown that plant diversity can help mitigate impacts of climate change by increasing plant productivity and ecosystem stability1,2. Although soil temperature and its stability are key determinants of essential ecosystem processes related to water and nutrient uptake3 as well as soil respiration and microbial activity4, no study has yet investigated whether plant diversity can buffer soil temperature fluctuations. Using 18 years of a continuous dataset with a resolution of 1 minute ([~]795,312,000 individual measurements) from a large-scale grassland biodiversity experiment, we show that plant diversity buffers soil temperature throughout the year. Plant diversity helped to prevent soil heating in hot weather, and cooling in cold weather. Moreover, this effect of plant diversity increased over the 18-year observation period with the aging of experimental communities and was even stronger under extreme conditions, i.e., on hot days or in dry years. Using structural equation modelling, we found that plant diversity stabilized soil temperature by increasing soil organic carbon concentrations and, to a lesser extent, by increasing the plant leaf area index. We suggest that the diversity-induced stabilization of soil temperature may help to mitigate the negative effects of extreme climatic events such as soil carbon release, thus slow global warming.

ecology↗

bioRxiv2022

Single-gene resolution of diversity-driven community overyielding

In plant communities, diversity often increases community productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute the positive diversity effects to complementary niches occupied by different species or genotypes. However, the type of niche complementarity often remains unclear, including how complementarity is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to identify differences associated with positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we found that between-plant allelic differences at the AtSUC8 locus contribute strongly to mixture overyielding. The corresponding gene encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affected the biochemical activities of protein variants and resulted in different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying such genes important for ecosystem functioning may ultimately allow the linking of ecological processes to evolutionary drivers, help to identify the traits underlying positive diversity effects, and facilitate the development of high-performing crop variety mixtures in agriculture.

plant biology↗

bioRxiv2022

Positive effects of tree diversity on tropical forest restoration in a field-scale experiment

Experiments under controlled conditions have established that ecosystem functioning is generally positively related to levels of biodiversity, but it is unclear how widespread these effects are in real-world settings and whether they can be harnessed for ecosystem restoration. We used a long-term, field-scale tropical restoration experiment to test how the diversity of planted trees affected recovery measured across a 500 ha area of selectively logged forest using multiple sources of satellite data. Replanting with species rich mixtures of tree seedlings that had higher phylogenetic and functional diversity accelerated restoration rates. Our results are consistent with a positive relationship between biodiversity and ecosystem functioning in the lowland dipterocarp rainforests of SE Asia and demonstrate that using diverse mixtures of species can enhance initial recovery after logging.

ecology↗

bioRxiv2022

How enhancers regulate wavelike gene expression patterns: A novel enhancer prediction and live reporter system identifies an enhancer associated with the arrest of pair-rule waves in Tribolium

A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called enhancers. Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the Drosophila embryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expressions in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetle Tribolium castaneum) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. Here we establish the AP patterning of the short-germ beetle Tribolium as a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, we established an enhancer prediction system in Tribolium based on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, we discovered several Tribolium enhancers, and assessed the spatiotemporal activities of some of them in live embryos. We found our data consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expressions (that we call dynamic enhancers) and enhancers that stabilizes gene expressions (that we call static enhancers).

developmental biology↗

bioRxiv2022

Remote sensing-based forest modeling reveals positive effects of functional diversity on productivity at local spatial scale

O_LIForest biodiversity is critical for many ecosystem functions and services at plot scale, but it is uncertain how biodiversity influences ecosystem functioning across environmental gradients and contiguous larger areas. We used remote sensing and process-based terrestrial biosphere modeling to explore functional diversity-productivity relationships at multiple scales for a heterogeneous forest site in Switzerland. C_LIO_LIWe ran the biosphere model with empirical data about forest structure and composition derived from ground-based surveys, airborne laser scanning and imaging spectroscopy for the years 2006-2015 at 10x10-m spatial resolution. We then related the model outputs forest productivity to functional diversity under observed and experimental model conditions. C_LIO_LIFunctional diversity increased productivity significantly (p < 0.001) across all simulations at 20x20-m to 30x30-m scale, but at 100x100-m scale positive relationships disappeared under homogeneous soil conditions. C_LIO_LIWhereas local functional diversity was an important driver of productivity, environmental context (especially soil depth, texture and water availability) underpinned the variation of productivity (and functional diversity) at larger spatial scales. Integration of remotely-sensed information on canopy composition and structure into terrestrial biosphere models helps fill the knowledge gap about how plant biodiversity affects carbon cycling and biosphere feedbacks onto climate over large contiguous areas. C_LI

ecology↗

bioRxiv2022

Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies

Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called "replication factories"), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and show that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, especially polyprotein cleavage, and viral RNA synthesis may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the viral replication in vitro early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth. Author summaryPlus-strand RNA viruses comprise a large group of related and medically relevant viruses. The current global pandemic of COVID-19 caused by the SARS-coronavirus-2 as well as the constant spread of diseases such as dengue and chikungunya fever show the necessity of a comprehensive and precise analysis of plus-strand RNA virus infections. Plus-strand RNA viruses share similarities in their life cycle. To understand their within-host replication strategies, we developed a mathematical model that studies pan-viral similarities and virus-specific differences of three plus-strand RNA viruses, namely hepatitis C, dengue, and coxsackievirus. By fitting our model to in vitro data, we found that only small virus-specific variations in the model were required to describe the dynamics of all three viruses. Furthermore, our model predicted that ribosomes involved in viral RNA translation seem to be a key player in plus-strand RNA replication efficiency, which may determine acute or chronic infection outcome. Furthermore, our in-silico drug treatment analysis suggests that targeting viral proteases involved in polyprotein cleavage, in combination with viral RNA replication, may represent promising drug targets with broad-spectrum antiviral activity.

microbiology↗

bioRxiv2022

Individual tree-based vs pixel-based approaches to mapping forest functional traits and diversity by remote sensing

Trait-based approaches, focusing on the functional characteristics of vascular plants in a community, have been increasingly used in plant ecology and biodiversity research. Compared with traditional field survey (which typically samples individual trees), remote sensing enables quantifying functional traits over large contiguous areas, but assigning trait values to biological units such as species and individuals is difficult with pixel-based approaches. We used a subtropical forest landscape in China to compare an approach based on LiDAR-delineated individual tree crowns (ITCs) with a pixel-based approach for assessing functional traits from remote sensing data. We compared trait distributions, trait-trait relationships and functional diversity metrics obtained by the two approaches at changing grain and extent. We found that morphological traits derived from airborne laser scanning showed more differences between ITC- and pixel-based approaches than physiological traits estimated by imaging spectroscopy data. Pixel sizes approximating average tree crowns yielded similar results as ITCs, but 95th quantile height and foliage height diversity tended to be overestimated and leaf area index underestimated relative to ITC-based values. With increasing pixel size, the differences to ITC- based trait values became larger and less trait variance was captured, indicating information loss. The consistency of ITC- and pixel-based functional richness measures also decreased with increasing pixel grain, and changed with the observed extent for functional diversity monitoring. We conclude that whereas ITC-based approaches in principle allow partitioning of variation between individuals, genotypes and species, at high resolution, pixel-based approaches come close to this and can be suitable for assessing ecosystem-scale trait variation by weighting individuals and species according to coverage.

ecology↗

bioRxiv2022

Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks

Addressing global biodiversity loss requires an expanded focus on multiple dimensions of biodiversity. While most studies have focused on the consequences of plant interspecific diversity, our mechanistic understanding of how the diversity within a given plant species (genetic diversity) affects plant productivity remains limited. Here, we use a tree species x genetic diversity experiment to disentangle the effects of species diversity and genetic diversity, and how they are related to tree functional diversity and trophic feedbacks. Tree species as well as genetic diversity increased tree productivity via increased tree functional diversity, reduced soil fungal diversity and marginally reduced herbivory. The effect of tree genetic diversity on productivity was partly different between tree species monocultures and mixtures: the functional diversity effect resulting from tree genetic diversity was only found in tree species monocultures, but the trophic feedbacks via herbivory were similar in species monocultures and mixtures. Given the complexity of interactions between tree species and genetic diversity, tree functional diversity and trophic feedbacks on productivity, we suggest that both tree species and genetic diversity should be considered in reforestation.

ecology↗

bioRxiv2021

Dominant species determine ecosystem stability across scales in Inner Mongolian grassland

There is an urgent need to extend knowledge on ecosystem temporal stability to larger spatial scales because presently available local-scale studies generally do not provide effective guide for management and conservation decisions at the level of an entire region with diverse plant communities. We investigated temporal stability of plant biomass production across spatial scales and hierarchical levels of community organization and analyzed impacts of dominant species, species diversity and climatic factors using a multi-site survey of Inner Mongolian grassland. We found that temporal stability at a large spatial scale, i.e. a large area aggregating multiple local communities, was related to temporal stability of and asynchrony among spatially separated local communities and large-scale population dynamics of dominant species, yet not to species richness. Additionally, a lower mean and higher variation of yearly precipitation destabilized communities at local and large scales by destabilizing dominant species population dynamics. We argue that, for semi-arid temperate grassland, dynamics and precipitation responses of dominant species and asynchrony among local communities stabilize ecosystems at large spatial scales. Our results indicate that reduced amounts and increased variation of precipitation may present key threats to the sustainable provision of biological products and services to human well-being in this region.

ecology↗

bioRxiv2021

A simple method to separate birds and insects in single-pol weather radar data

Recent and archived data from weather radar networks are extensively used for quantification of continent-wide bird migration pattern. While discriminating birds from weather signals is well established, insect contamination is still a problem. We present a simple method combining two doppler radar products within a single Gaussian-mixture model to estimate the proportions of birds and insects within a single measurement, as well as the density and speed of birds and insects. The method can be applied to any existing archives of vertical bird profiles, such as the ENRAM repository (enram.eu) with no need to recalculate the huge amount of original polar volume data, which often are not available.

ecology↗

bioRxiv2021

Myelin biogenesis is associated with pathological ultrastructure that is resolved by microglia during development

To enable rapid propagation of action potentials, axons are ensheathed by myelin, a multilayered insulating membrane formed by oligodendrocytes. Most of the myelin is generated early in development, in a process thought to be error-free, resulting in the generation of long-lasting stable membrane structures. Here, we explored structural and dynamic changes in CNS myelin during development by combining ultrastructural analysis of mouse optic nerves by serial block face scanning electron microscopy and confocal time-lapse imaging in the zebrafish spinal cord. We found that myelin undergoes extensive ultrastructural changes during early postnatal development. Myelin degeneration profiles were engulfed and phagocytosed by microglia in a phosphatidylserine-dependent manner. In contrast, retractions of entire myelin sheaths occurred independently of microglia and involved uptake of myelin by the oligodendrocyte itself. Our findings show that the generation of myelin early in development is an inaccurate process associated with aberrant ultrastructural features that requires substantial refinement.

neuroscience↗

bioRxiv2021

Hydraulic diversity stabilizes productivity in a large-scale subtropical tree biodiversity experiment

Extreme climatic events threaten forests and their climate mitigation potential globally. Understanding the drivers promoting ecosystem stability is therefore considered crucial to mitigate adverse climate change effects on forests. Here, we use structural equation models to explain how tree species richness, asynchronous species dynamics and diversity in hydraulic traits affect the stability of forest productivity along an experimentally manipulated biodiversity gradient ranging from 1 to 24 tree species. Tree species richness improved stability by increasing species asynchrony. That is, at higher species richness, inter-annual variation in productivity among tree species buffered the community against stress-related productivity declines. This effect was mediated by the diversity of species hydraulic traits regarding drought tolerance and stomatal control, but not by the community-weighted means of these traits. The identified mechanisms by which tree species richness stabilizes forest productivity emphasize the importance of hydraulically diverse, mixed-species forests to adapt to climate change.

ecology↗

bioRxiv2021

Apomixis and genetic background affect distinct traits in Hieracium pilosella L. grown under competition

BackgroundApomixis, the asexual reproduction through seeds, occurs in over 40 plant families and avoids the hidden cost of sex. Apomictic plants are thought to have an advantage in sparse populations and when colonizing new areas but may have a disadvantage in changing environments because they propagate via fixed genotypes. In this study, we separated the influences of different genetic backgrounds (potentially reflecting local adaptation) from those of the mode of reproduction, i.e., sexual vs. apomictic, on nine fitness-related traits in Hieracium pilosella L. We aimed to test whether apomixis per se may provide a fitness advantage in different competition environments in a common garden setting. ResultsTo separate the effects of genetic background from those of reproductive mode, we generated five families of apomictic and sexual full siblings by crossing two paternal with four maternal parents. Under competition, apomictic plants showed reproductive assurance (probability of seeding, fertility), while offspring of sexual plants with the same genetic background had a higher germination rate. Sexual plants grew better (biomass) than apomictic plants in the presence of grass as a competitor but apomictic plants spread further vegetatively (maximum stolon length) when their competitors were sexual plants of the same species. Furthermore, genetic background as represented by the five full-sibling families influenced maximum stolon length, the number of seeds, and total fitness. Under competition with grass, genetic background influenced fecundity, the number of seeds, and germination rate. ConclusionsOur results suggest that both the mode of reproduction as well as the genetic background affect the success of H. pilosella in competitive environments. Total fitness, the most relevant trait for adaptation, was only affected by the genetic background. However, we also show for the first time that apomixis per se has effects on fitness-related traits that are not confounded by -- and thus independent of -- the genetic background.

plant biology↗

bioRxiv2020

APOE4 affects basal and NMDAR mediated protein synthesis in neurons by perturbing calcium homeostasis

Apolipoprotein E (APOE), one of the primary lipoproteins in the brain has three isoforms in humans - APOE2, APOE3, and APOE4. APOE4 is the most well-established risk factor increasing the pre-disposition for Alzheimers disease. The presence of the APOE4 allele alone is shown to cause synaptic defects in neurons and recent studies have identified multiple pathways directly influenced by APOE4. However, the mechanisms underlying APOE4 induced synaptic dysfunction remain elusive. Here, we report that the acute exposure of primary cortical neurons to APOE4 leads to a significant decrease in global protein synthesis. APOE4 treatment also abrogates the NMDA mediated translation response indicating an impairment of synaptic signaling. Importantly, we demonstrate that both APOE3 and APOE4 generate a distinct translation response which is closely linked to their respective calcium signature. Acute exposure to APOE3 causes a short burst of calcium through NMDARs in neurons leading to an initial decrease in protein synthesis which quickly recovers. Contrarily, APOE4 leads to a sustained increase in calcium levels by activating both NMDARs and L-VGCCs, thereby causing sustained translation inhibition through eEF2 phosphorylation, which in turn disrupts NMDAR response. Thus, we show that APOE4 affects basal and activity mediated protein synthesis response in neurons by affecting calcium homeostasis. We propose this as a possible mechanism to explain the synaptic dysfunction caused by APOE4. Highlights / SummaryO_LIAPOE3 treatment causes a short burst of calcium through NMDARs, leading to an acute increase in eEF2 phosphorylation which eventually recovers to basal levels. C_LIO_LIGlobal translation follows a similar temporal profile of initial inhibition followed by recovery in APOE3 treated neurons, thus unaffecting the NMDA mediated translation response. C_LIO_LIAPOE4 treatment activates both NMDARs and L-VGCCs leading to a marked elevation in calcium levels, thus causing sustained increase in eEF2 phosphorylation as well as global translation inhibition. C_LIO_LIHence, the NMDA mediated response is perturbed, potentially causing a stress-related phenotype in APOE4 treated neurons. C_LIO_LIThus, different calcium signatures and sources lead to distinct temporal profiles of translation. C_LI

neuroscience↗

bioRxiv2020

Modelling the flow of nocturnal bird migration with year-round European weather radar network

The movements of migratory birds constitute huge biomass flows that influence ecosystems and human economy, agriculture and health through the transport of energy, nutrients, seeds, and parasites. To better understand the influence on ecosystems and the corresponding services and disservices, we need to characterize and quantify the migratory movements at various spatial and temporal scales. Representing the flow of birds in the air as a fluid, we applied a flow model to interpolated maps of bird density and velocity retrieved from the European weather radar network, covering almost a full year. Using this model, we quantified how many birds take-off, fly, and land across Western Europe, (1) to track waves of bird migration between nights, (2) cumulate the number of bird on the ground and (3) quantify the seasonal flow into and out of the study area through several regional transects. Our results show that up to 188 million (M) birds take-off over a single night. Exemplarily, we tracked a migration wave in spring, in which birds crossed the study area in 4 days with nocturnal flights of approximately 300 km. Over the course of a season, we estimated that 494 million (M) birds entered through the southern transects and, at the same time, 251 M left in the northern transects, creating a surplus of 243 M birds within the study area. Similarly, in autumn, 544 M more birds departed than arrived: 314 M birds entered through the northern transects while 858 M left through the southern transects. Our study show-cases the potential of combining interdisciplinary data and methods to elucidate the dynamics of avian migration from nightly to seasonal and yearly time-scales and from regional to continental spatial scales.

ecology↗

bioRxiv2020

Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning

Theoretical and empirical advances have revealed the importance of biodiversity for stabilizing ecosystem functions through time. Yet despite the global degradation of soils, how the loss of soil microbial diversity can de-stabilizes ecosystem functioning is unknown. Here we experimentally quantified the contribution diversity and the temporal dynamics in the composition of soil microbial communities to the temporal stability of four key ecosystem functions related to nutrient and carbon cycling. Soil microbial diversity loss reduced the temporal stability of all ecosystem functions and was particularly strong when over 50% of microbial taxa were lost. The stabilizing effect of soil biodiversity was linked to asynchrony among microbial taxa whereby different soil fungi and bacteria were associated with different ecosystem functions at different times. Our results emphasize the need to conserve soil biodiversity in order to ensure the reliable provisioning of multiple ecosystems functions that soils provide to society.

ecology↗

bioRxiv2020

A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation

Granulin (GRN) is a pleiotropic protein involved in inflammation, wound healing, neurodegenerative disease, and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis, frontotemporal dementia, and to enhance wound healing. How granulin contributes to each of these diverse biological functions, however, remains largely unknown. Here, we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency, we reveal that in the absence of granulin a (grna), myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages during normal and emergency myelopoiesis. In addition, macrophages fail to recruit to the wound, resulting in abnormal healing. Our CUT&RUN experiments identify Pu.1, which together with Irf8 positively regulate grna expression. Importantly, we demonstrate functional conservation between the mammalian granulin and the zebrafish orthologue grna. Our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation, opening a new field of study that has the potential to impact different aspects of the human health.

cell biology↗