Biology subjects

Schreiber, L.

Publications and source records attributed to Schreiber, L..

9 recordsLinked to original sources

bioRxiv2026

Potassium deficiency reinforces the endodermal but not the exodermal suberized barrier in maize seminal roots

Potassium (K) deficiency is a widespread constraint on maize production, yet how it influences the suberized apoplastic barriers that control radial K transport in roots, and whether the endodermis and the constitutively suberized exodermis respond differently, has remained unclear. We grew maize under K deficiency in soil and across a hydroponic K gradient, with abscisic acid (ABA) and fluridone treatments, and analysed seminal roots by Fluorol Yellow 088 staining, tissue-resolved suberin chemistry of endodermis and exodermis, rubidium (Rb) flux, and RNA-sequencing with weighted gene co-expression network analysis (WGCNA). K deficiency selectively increased endodermal aliphatic suberin and eliminated endodermal passage cells in soil-grown roots, whereas exodermal suberin was unchanged. Although K influx remained high, root-to-shoot Rb translocation fell sharply, consistent with K retention. A single co-expression module linked the suberin-biosynthetic genes with several K transport genes, and the suberin programme responded to exogenous ABA, indicating ABA-dependent co-regulation. Soil and hydroponic systems converged on the same endodermis-specific anatomical response. Endodermal, but not exodermal, barrier reinforcement limits K leakage from the stele in maize roots. This tissue-specific plasticity identifies the endodermal suberin biosynthesis programme, and its coordination with K uptake, as a target for improving K use efficiency.

plant biology↗

bioRxiv2026

AncientMetagenomeDir dating metadataset highlights need for standardised radiocarbon reporting in ancient DNA

Ancient DNA is a valuable data source for the understanding of our past. However, to effectively interpret this data, it is essential to know the age of the samples from which the DNA is obtained. Although the field of palaeogenomics has been recognised for its robust open data sharing practices, dating information associated with analysed samples is not reported consistently across palaeogenomic studies, nor is it included as metadata in most genetic data repositories. Here, we describe the addition of standardised precise dating information for ancient microbial genomes into the AncientMetagenomeDir metadata repository of published ancient metagenomic samples. This extension currently includes dating information for over 700 ancient microbial genomic datasets, of which 333 are dated using historical, contextual, or stratigraphic methods, and 405 are radiocarbon dated. We quantitatively assess the quality of radiocarbon date reporting and find that, despite established reporting conventions, radiocarbon dating information is often reported inconsistently across ancient metagenomic studies. This new resource provides ancient microbial researchers with standardised dating information that facilitates more accurate and consistent analysis of metagenomic sequencing data. The dataset also highlights the need for greater standardisation of radiocarbon date reporting in original publications in order to allow effective reuse of this and future ancient microbial data.

bioinformatics↗

bioRxiv2025

QUILPEN provides independent and label-free single-cell quantification of pigmentation dynamics and organelle content

The relationship between melanogenesis, pigmentation, and melanocyte behavior is complex. In melanocytes, pigmentation is often associated with differentiation, yet mature melanocytes vary in pigment content. In melanoma, pigmentation-linked transcriptional programs may have prognostic value, but visual assessments of tumor pigmentation have yielded inconsistent results. Progress linking pigmentation phenotypes to cell state has been limited by a lack of tools that can directly and dynamically quantify melanin content in live cells. Here we present QUantitative Imaging of Label-free Pigment-associated ENtities (QUILPEN), a label-free multi-modal imaging technique that combines quantitative phase imaging (QPI), quadrant darkfield (QDF), and absorption imaging, to independently capture light that has been transmitted, scattered, and absorbed. This non-destructive method enables live-cell imaging over multiple days without labels. We show absorption as a reliable readout of melanin content, which can be decoupled from melanosome content detected by QDF, which measures scattered light. Applying QUILPEN to melanoma cells before and during repigmentation, we find that melanin content is highly heterogeneous, and that this heterogeneity is reinstated upon repigmentation. Lineage tracking further reveals that melanin synthesis rates are heritable and can be transmitted both symmetrically and asymmetrically. QUILPEN enables real-time quantification of pigmentation dynamics and cell-level heterogeneity. SignificancePigmentation is a defining feature of melanocytic cells and linked to behavior, yet melanins optical properties complicate direct measurement with existing approaches. Taking advantage of the absorbing nature of pigment and scattering properties of organelles, we can independently track pigment and organelle content over time and along cell lineages in a label-free manner to reveal population heterogeneity and patterns of inheritance. Research HighlightsQUILPEN is a label-free, live cell imaging pipeline that independently quantifies pigment and organelles in melanocytic cells. Tracking pigment and organelle content along cell lineages reveals varied inheritance of pigment-associated features. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/683473v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@8d1ef9org.highwire.dtl.DTLVardef@ec6ebdorg.highwire.dtl.DTLVardef@5a7b64org.highwire.dtl.DTLVardef@5b0d80_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Regulatory Analysis of Root Architectural and Anatomical Adaptation to Nitrate and Ammonium in Brachypodium distachyon

Root system architecture plays an important role in nitrate and ammonium uptake, the two primary nitrogen (N) forms essential for plant growth. Plants deploy different strategies to optimize the N uptake by roots, based on a complicated regulatory network that controls root phenotype and physiology. Here, we studied the response of root architecture to varying N applications in the model species Brachypodium distachyon. Using a combination of phenotypic and transcriptomic analyses, we examined how different forms and concentrations of ammonium and nitrate affect root growth, biomass allocation, and N uptake. N concentrations significantly influence root traits such as root length, root hair development, and aerenchyma formation in response to nitrate and ammonium. Plants grown in ammonium conditions had thin but highly branched roots, whereas nitrate application resulted in shorter, thicker roots with denser root hair at higher nitrate concentrations. Furthermore, using advanced co-expression network analysis, we identified an Atypical Aspartic Protease (APs) gene encoding an aspartyl protease family protein and a phosphoenolpyruvate carboxylase 1 (PEPC1) gene in brachypodium, which potentially control the root architectural and anatomical adaptions to different N form. APs expression showed a positive correlation with total root length and lateral root development, along with a negative correlation with root hair density. In contrast, PEPC1 exhibited positive correlations with cortex, stele, root cross-sectional areas, and root hair density, while showing a negative correlation with total root length. These genes likely play an important role in the transcriptional regulatory networks involved in these adaptive responses, which highlight the complex interplay between root morphology, nitrogen metabolism, and environmental nutrient conditions.

plant biology↗

bioRxiv2024

Aluminium induces suberin biosynthesis in barley roots via ABA

Aluminum (Al) toxicity is a major factor limiting plant growth in acidic soils. The beneficial element silicon (Si) can mitigate some effects of Al. However, the impact of Al on suberized apoplastic barriers in roots are largely unknown while the effects of Si on suberin remains controversial. This study employed physiological, histochemical, and analytical methods, along with Laser Capture Microdissection (LCM) RNA-sequencing, to explore the effects of Al and Si on suberin development in barley (Hordeum vulgare L.), a species sensitive to Al stress. Exposure of barley seedlings to Al resulted in increased suberin deposition, which could be restored with the addition of Si, particularly in the root endodermis. Gene expression analyses using LCM RNA-seq across different root tissues demonstrated that Al-induced suberin biosynthesis is mainly regulated by the abscisic acid (ABA) pathway. In addition, the application of fluridone, an inhibitor of ABA synthesis and a suberin mutant, further supported the pivotal role of ABA in the Al response and the role of suberin in influencing Al uptake. Our findings underscore the complex interplay between Al stress and suberin biosynthesis in barley, providing insights into potential strategies for enhancing crop resilience to Al toxicity.

plant biology↗

bioRxiv2023

Hitching a ride in the phyllosphere: Surfactant production of Pseudomonas spp. causes co-swarming of Pantoea eucalypti 299R

Here we demonstrate the beneficial effect of surfactant-producing Pseudomonads on the phyllosphere model strain Pantoea eucalypti 299R. To do so, we conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R and Pseudomonas sp. FF1 (Pff1) or P. eucalypti 299R and the surfactant-deficient mutant P. sp. FF1::{Delta}viscB (Pff1{Delta}viscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of P. eucalypti 299R when growing in the presence of Pff1 or Pff1{Delta}viscB. By contrast, on swarming agar plates, P. eucalypti was able to co-swarm with Pff1. Co-swarming led to a significant increase in the area colonized and, consequently, a boost in total biomass when compared to P. eucalypti growing with Pff1{Delta}viscB or in monoculture. Finally in planta, there were no significant effects on the population density of P. eucalypti 299R during co-colonization of Arabidopsis thaliana. However, utilizing the single cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated P. eucalypti 299R subpopulations that did not occur in presence of Pff1{Delta}viscB. This led us to formulate a model for the positive effect of surfactant production during leaf colonization. To generalize our results, we tested the effect of three additional surfactant-producing Pseudomonads and their respective surfactant knockout mutants on P. eucalypti 299R on swarming agar. Resulting in similar co-swarming patterns in P. eucalypti 299R and showing that this organism is able to take advantage of competitors during surface colonization. Our results indicate that surfactant-dependent co-motility might be common during leaf colonization and add yet another facet to the already manyfold roles of surfactants.

microbiology↗

bioRxiv2022

The lectin receptor Clec4F participates in the capture of circulating parasite mucins by Kupffer cells in cystic echinococcosis.

Cystic echinococcosis is caused by the larval stages (hydatids) of cestode parasites belonging to the species cluster Echinococcus granulosus sensu lato, with E. granulosus sensu stricto being the main infecting species. Hydatids are bladder-like structures that attain large sizes within various internal organs of livestock ungulates and humans. Hydatids are protected by the massive acellular laminated layer (LL), composed mainly by mucins. Parasite growth requires LL turnover, and abundant LL-derived particles are found at infection sites in infected humans, raising the question of how LL materials are dealt with by the hosts. In this article, we show that E. granulosus sensu stricto LL mucins injected into mice are taken up by Kupffer cells, the liver macrophages exposed to the vascular space. This uptake is largely dependent on the intact mucin glycans and on Clec4F, a C-type lectin receptor which in rodents is selectively expressed in Kupffer cells. This uptake mechanism operates on mucins injected both in soluble form i.v. and in particulate form i.p. In mice harbouring intraperitoneal infections by the same species, LL mucins were found essentially only at the infection site and in the liver, where they were taken up by Kupffer cells via Clec4F. Therefore, shed LL materials circulate in the host and Kupffer cells can act as a sink for these materials even when the parasite grows in sites other than the liver.

immunology↗

bioRxiv2022

Rational design yields molecular insights on leaf binding of the anchor peptide Macaque Histatin

1In times of a constantly growing world population and increasing demand for food, sustainable agriculture is crucial. To reduce the amount of applied nutrients, herbicides, and fungicides, the rainfastness of plant protection agents is of pivotal importance. As a result of protective agent wash-off, plant protection is lost, and soils and groundwater are severely polluted. To date, rainfastness of plant protection products is achieved by adding polymeric adjuvants to the agrochemicals. However, polymeric adjuvants will be regarded as microplastics in the future, and environmentally friendly alternatives are needed. Anchor peptides (APs) are promising biobased and biodegradable adhesion promoters. While the adhesion of anchor peptides to artificial surfaces, such as polymers, has already been investigated in theory and experimentally, exploiting the adhesion to biological surfaces remains challenging. The complex nature and composition of biological surfaces such as plant leaf and fruit surfaces complicate the generation of accurate models. Here, we present the first detailed three-layered atomistic model of the surface of apple leaves and use it to compute free energy profiles of the adhesion and desorption of APs to and from that surface. Our model is validated by a novel fluorescence-based MTP assay that mimicks these complex processes and allows quantifying them. For the AP Macaque Histatin, we demonstrate that aromatic and positively charged amino acids are essential for binding to the waxy apple leaf surface. The established protocols should generally be applicable for tailoring the binding properties of APs to biological interfaces.

bioengineering↗

bioRxiv2020

Characterisation of the biosurfactants from phyllosphere colonising Pseudomonads and their effect on plant colonisation and diesel degradation

Biosurfactant production is a common trait in leaf surface colonising bacteria that has been associated with increased survival and movement on leaves. At the same time the ability to degrade aliphatics is common in biosurfactant-producing leaf colonisers. Pseudomonads are common leaf colonisers and have been recognised for their ability to produce biosurfactants and degrade aliphatic compounds. In this study, we have investigated the role of biosurfactants in four non-plant plant pathogenic Pseudomonas strains by performing a series of experiments to characterise the surfactant properties, and their role during leaf colonisation and diesel degradation. The produced biosurfactants were identified using mass-spectrometry. Two strains produced viscosin-like biosurfactants and the other two produced Massetolide A-like biosurfactants which aligned with the phylogenetic relatedness between the strains. To further investigate the role of surfactant production, random Tn5 transposon mutagenesis was performed to generate knockout mutants. The knockout mutants were compared to their respective wildtypes in their ability to colonise gnotobiotic Arabidopsis thaliana and to degrade diesel. It was not possible to detect negative effects during plant colonisation in direct competition or individual colonisation experiments. When grown on diesel, knockout mutants grew significantly slower compared to their respective wildtypes. By adding isolated wildtype biosurfactants it was possible to complement the growth of the knockout mutants. ImportanceMany leaf colonising bacteria produce surfactants and are able to degrade aliphatic compounds, however, if surfactant production provides a competitive advantage during leaf colonisation is unclear. Furthermore, it is unclear if leaf colonisers take advantage of the aliphatic compounds that constitute the leaf cuticle and cuticular waxes. Here we test the effect of surfactant production on leaf colonisation and demonstrate that the lack of surfactant production decreases the ability to degrade aliphatic compounds. This indicates that leaf surface dwelling, surfactant producing bacteria contribute to degradation of environmental hydrocarbons and may be able to utilise leaf surface waxes. This has implications for plant-microbe interactions and future studies.

microbiology↗