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T7 RNA polymerase-based gene expression from a transcriptionally silent rDNA spacer in the endosymbiont-harboring trypanosomatid Angomonas deanei

In vivo online monitoring of intracellular lipid accumulation in Ustilago maydis

MAdLand Project - Wolfgang Hess Lab

Charophyceae are the most complex streptophyte algae, possessing tissue-like structures, rhizoids and a cellulose-pectin-based cell wall akin to embryophytes. Together with the Zygnematophyceae and the Coleochaetophycae, the Charophyceae form a grade in which the Zygnematophyceae share a last common ancestor with land plants. The availability of genomic data, its short life cycle, and the ease of non-sterile cultivation in the laboratory have made the species Chara braunii an emerging model system for streptophyte terrestrialization and early land plant evolution. In this study, tissue containing nodal cells was prepared under the stereomicroscope, and an RNA-seq dataset was generated and compared to transcriptome data from whole plantlets. In both samples, transcript coverage was high for genes encoding ribosomal proteins and a homolog of the putative PAX3- and PAX7-binding protein 1. Gene ontology was used to classify the putative functions of the differently expressed genes. In the nodal cell sample, main upregulated molecular functions were related to protein, nucleic acid, ATP- and DNA binding. Looking at specific genes, several signaling-related genes and genes encoding sugar-metabolizing enzymes were found to be expressed at a higher level in the nodal cell sample, while photosynthesis-and chloroplast-related genes were expressed at a comparatively lower level. We detected the transcription of 21 different genes encoding DUF4360-containing cysteine-rich proteins. The data contribute to the growing understanding of Charophyceae developmental biology by providing a first insight into the transcriptome composition of Chara nodal cells.

Physiologia Plantarum / Volume 175, Issue 5 / e14025, https://doi.org/10.1111/ppl.14025

Physiology, biochemistry and anatomy of young fully developed leaves from Brassicaceae species with C3 and C3-C4 (C2) photosynthesis

GP-rapid, a newly developed fast-cycling barley genotype, reduces generation time by 25% while remaining amenable to transformation, advancing functional genomic studies in barley.

Integrating landscape transcriptomics approach, in-situ trait phenotyping, and machine learning to unravel genes associated with ecologically relevant traits.

This research investigates the effects of potato glycoalkaloids (PGAs), α-solanine and α-chaconine, on growth and survival of plant pathogens and beneficial organisms from different biological groups.

Seeds should not germinate in conditions unsuitable for seedling growth. Dormancy, which allows seeds to remain inactive in an environment that would otherwise enable germination, helps optimise the timing of germination. Primary dormancy, developed during seed maturation on the parent plant, prevents immediate germination post-dispersal, regardless of external conditions. Secondary dormancy, however, is triggered post-dispersal when seeds face unfavourable conditions, enabling them to re-enter dormancy even if initially non-dormant. This mechanism allows seeds to fine-tune germination according to environmental conditions. In this study, we examined the role of heat-induced secondary dormancy in local adaptation by analysing natural variations within 361 Arabidopsis thaliana accessions from across Europe. We discovered that secondary dormancy acquisition varies with primary dormancy levels and after-ripening. Both primary and heat-induced secondary dormancy exhibited adaptive clines along temperature and precipitation gradients, with secondary dormancy showing a steeper cline, indicating its significant role in local adaptation. Using species distribution models, we predicted that genotypes with high secondary dormancy would show greater resilience to future climate changes. Additionally, we identified specific genomic regions controlling secondary dormancy levels including a novel candidate gene for secondary dormancy variation. Our findings show that secondary dormancy is a complex adaptive mechanism and a predominant contributor to the dormancy trait syndrome that favours plant survival in habitats exposed to harsh summers.

Lipidomics analysis of bacterial acyltransferase chiral substrate specificity

As environmental change accelerates in the Anthropocene, a central challenge in evolutionary biology is understanding how populations respond to novel and rapidly changing conditions. Adaptation underpins whether species can persist and diverge under increasingly variable selective pressures. While adaptive potential is often inferred from phenotypic change or standing genetic variation, it remains unclear what determines the evolutionary “fuel” that enables sustained response. Using Arabidopsis species as model systems, this thesis examines the genetic basis of adaptation and how variation is generated and structured across biological scales, from life-history traits to gene expression and genomic interactions, with a particular focus on how genetic architecture shapes the pace and predictability of evolutionary change.

Together, this work conceptualises adaptive potential as an emergent population-level property arising from interactions among ecological traits, genetic architecture, molecular regulation, and environmental context. Adaptive potential depends not on the amount of variation present, but on its structure, heritability, and exposure to selection across evolutionary timescales.

This project characterizes the genomic integrity of Escherichia coli K-12 through a comprehensive workflow spanning bacterial cultivation, DNA extraction, library preparation, Illumina sequencing, and bioinformatic analysis. The integrated approach ensures high-quality genome assemblies consistent with the reference strain.

In seed plants, a tethering complex of two proteins, SEED LIPID DROPLET PROTEIN (SLDP) and LIPID DROPLET PLASMA MEMBRANE ADAPTOR (LIPA), binds lipid droplets (LDs) to the plasma membrane (PM). While the physiological function remains obscure, the conservation of the process is strong. The tethering of LDs can be observed broadly in a variety of seed plants seedling tissues. Interestingly a tethering might not be limited to the PM and could be associated with other organelles in other plants. Here, we show that LIPA and SLDP have emerged in the early period of land plant evolution likely before the emerging seed plants became dominant. They are, however, most prominently conserved in seed plants and their homologs share the tethering function in ectopic expression systems. This interaction is robust and can even be functional across taxon boundaries. The evolution of a LD PM tether in that significant time point also puts the LD in focus of land plant evolution. The involvement of LDs in conquest of terrestrial ecosystems and the studying thereof can give valuable insight in physiological processes that made early terrestrialization events possible. Further studies need to evaluate the function of the discovered homologs in non-seed plants.

MAdLand Project - Schippers Lab

Evolutionary conserved and divergent responses to copper zinc superoxide dismutase inhibition in plants

After initial evolution in a reducing environment, life got successively challenged by reactive oxygen species (ROS), especially during the great oxidation event (GOE) that followed the development of photosynthesis. Therefore, ROS are deeply intertwined into the physiological, morphological and transcriptional responses of most present-day organisms. Copper-zinc superoxide dismutase (CuZnSOD) evolved during the GOE and are present in charophytes and extant land plants, but nearly absent from chlorophytes. The chemical inhibitor of CuZnSOD, lung cancer screen 1 (LCS-1), could greatly facilitate the study of SODs in diverse plants. Here, we determined the impact of chemical inhibition of plant CuZnSOD activity, on plant growth, transcription and metabolism. We followed a comparative approach by using different plant species, including Marchantia polymorpha and Physcomitrium patens, representing bryophytes, the sister lineage to vascular plants, and Arabidopsis thaliana. We show that LCS-1 causes oxidative stress in plants and that the inhibition of CuZnSODs provoked a similar core response that mainly impacted glutathione homeostasis in all plant species analyzed. That said, Physcomitrium and Arabidopsis, which contain multiple CuZnSOD isoforms showed a more complex and exacerbated response. In addition, an untargeted metabolomics approach revealed a specific metabolic signature for each plant species. Our comparative analysis exposes a conserved core response at the physiological and transcriptional level towards LCS-1, while the metabolic response largely varies. These differences correlate with the number and localization of the CuZnSOD isoforms present in each species.

Plant, Cell & Environment (in submission)

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This ARC contains data and instruction to recapitulate bioinformatics pipelines excecuted in the manuscript [comment: insert final link] Cis-regulatory architecture downstream of FLOWERING LOCUS T underlies quantitative control of flowering in Arabidopsis thaliana by Hao-Ran Zhou (周豪然), Duong Thi Hai Doan, Thomas Hartwig and Franziska Turck, published in Genome Biology (2026).

The amplitude between the minimum and the maximum ambient temperature a plant has to endure during its life cycle is much larger in terrestrial than in aquatic environments. As such, especially elevated ambient temperatures are among the most prominent abiotic factors plants had to cope with to successfully colonize land. It is known that the phenotypic plasticity in eudicot land plants allows them to adjust shoot architecture to acclimate and adapt to elevated temperatures. How and when this mechanism, thermomorphogenesis, has originated is unknown. Likewise, we do not know whether bryophytes, whose body plans is probably very similar to that of the first terrestrial plants, perform thermomorphogenesis. In this project, we will therefore characterize the response of bryophytes (Physcomitrium patens and Marchantia polymorpha) to elevated temperatures on both the morphological as well as the physiological level, including elucidation of temperature sensitive signaling cascades. In addition to comparative analyses we will also follow an unbiased approach, primarily using the liverwort Marchantia polymorpha. To identify signaling and response modules, we will generate high density transcriptomic and phosphoproteomic datasets and use them to construct gene regulatory networks based on machine learning approaches. As such, we aim to combine morphological and molecular data in this project to better understand how bryophytes cope with elevated ambient temperatures. With this knowledge. we might then be in a position to design experiments that directly address the emergence of such mechanisms and their role during the terrestrialization of land by plants.