Biology subjects

Schulz, P.

Publications and source records attributed to Schulz, P..

8 recordsLinked to original sources

bioRxiv2025

Discovery of a Novel Chimeric Transposase-Transposon System for Advanced Genome Engineering

Transposases revolutionized the field of genetic engineering, yet the scarcity of functional systems remains a challenge. In response, we conducted a metagenomic screening and identified a novel transposase system from Acyrthosiphon pisum. Through systematic optimization, we enhanced nuclear localization, transposon composition, and created a hyperactive transposase variant to boost transposition efficiency. Intriguingly, the combined application of the newly discovered transposase with inverted terminal repeat sequences from a related pea aphid species, Aphis craccivora, further enhanced transposition activity, resulting in the first chimeric transposase system reported so far. We investigated the genomic integration events following transposition in mammalian cells, to understand the underlying mechanisms and optimize the efficiency of transgene integration. This optimized system can expedite the generation of recombinant protein producing CHO cell lines, even surpassing the hyperactive piggyBac system with regards to cell specific productivity. These findings introduce a significant addition to the field of semi-targeted transgene integration technologies, offering substantial potential for enhancing biologics manufacturing.

bioengineering↗

bioRxiv2025

An integrated platform for high-throughput phenospace learning of 3D multilineage organoid systems

Complex multilineage organoid systems lack quantitative phenotyping methods preserving spatial architecture at high throughput. Current approaches compromise biological complexity, spatial resolution, or robust homogeneous multilineage assembly. We establish an integrated experimental-computational platform for high-throughput spatial phenotyping of multilineage organoids through developing a modular tumoroid culture system incorporating pancreatic ductal adenocarcinoma (PDAC) cells and cancer-associated fibroblasts (CAFs) in 384-well format with multiplexed whole-mount imaging. We developed Phenocoder, a machine learning framework combining conditional variational autoencoders with spatial graph analysis to extract multiscale organoid features. Rigorous validation demonstrates robust performance in PDAC tumoroids. The platform identifies pathway modulators that disrupt the fibrotic microenvironment and discovers stroma-dependent vulnerabilities, undetectable in monocultures. Extending to immuno-competent tumoroids, we assess fibrosis modulators in combination with T cell bispecific antibodies, identifying treatments that enhance immune cell proliferation and infiltration inducing cancer cell death, validated in patient-derived explants. This platform establishes a generalizable framework for multilineage organoid phenotyping.

cancer biology↗

bioRxiv2025

Tracking the evolutionary trajectory of a young hybrid plant pathogen

A common mechanism by which emerging plant pathogens gain the ability to infect new hosts is hybridization. Despite its widespread occurrence, the outcomes of hybridization remain largely unpredictable within current evolutionary frameworks, making empirical studies key for identifying patterns and establishing principles underlying hybrid evolution. Here, we track the evolutionary trajectory of Blumeria graminis forma specialis triticale (B.g. triticale), or triticale powdery mildew, a pathogen that emerged recently through hybridization of two powdery mildew forms specialized on wheat (B.g. tritici) and rye (B.g. secalis). Using a genomic dataset of 652 isolates from the three formae speciales, we show that they persist as three isolated lineages. Results from our infection assays and sampling suggest that B.g. triticale is not well adapted to infect wheat under field conditions, indicating that isolation between B.g. tritici and B.g. triticale may be maintained by partial niche separation. We investigated the genomic changes following hybridization and found that at least a third of the hybrid genome is fixed for B.g. tritici ancestry in contemporary populations, and around 1% is fixed for the B.g. secalis ancestry. We identified several loci to be under recent positive selection in B.g. triticale, most of which coincide with known genes and regions of fixed or nearly fixed local ancestry. Overall, we highlight the role of ecological isolation in preventing gene flow between B.g. triticale and its parental lineages. We reveal the rapid stabilization of its genome after hybridization and show that some of these changes were likely shaped by selection. Significance statementEmerging plant diseases pose serious risks to biodiversity and food production. A common mechanism by which fungal plant pathogens emerge on previously uncolonized hosts is hybridization. Hybridization brings together novel genetic combinations from different lineages that can facilitate adaptation to new environments. However, the evolutionary fate of hybrid pathogens is difficult to predict, and empirical studies of natural populations can help shed light on the dynamics of pathogen evolution following hybridization. Here, we use genomic data and infection assays to follow the evolutionary trajectory of a recently emerged hybrid plant pathogen. We show that the hybrid persists as an independent lineage distinct from both parents and analyze the genomic changes that have occurred in the few decades since initial hybridization.

evolutionary biology↗

bioRxiv2025

Carbonized rubber electrodes can cause a DC-offset in transcranial alternating current stimulation

IntroductionCarbonized rubber electrodes are widely used in non-invasive brain stimulation studies. Due to their polarizable nature, however, they can cause a voltage offset, which might be problematic for concurrent EEG studies. ObjectiveIn this study, we aim to describe the voltage offset and ensure that the offset does not alter the intended waveform of applied stimulation. MethodsUsing data from 2 human studies and phantom measurements, which employed carbonized rubber electrodes, we quantify the magnitude and frequency of DC-offsets and contrast this against pilot-measurements using Ag/AGCl-electrodes. In a further phantom study, we record the offset-voltage that arises from the electrode/electrolyte interface and compare this to the voltage put out by the stimulation device. ResultsA non-zero voltage offset is present in all human and phantom studies employing carbonized rubber electrodes, while the offset using Ag/AgCl electrodes is close to zero. Direct measurements of the stimulator output in the presence of a measurable voltage offset at the stimulation electrodes shows that the offset originates from the electrodes and not from the current provided by the stimulation device. ConclusionUsing carbonized rubber-electrodes for stimulation can result in the emergence of a measurable voltage offset, due to their polarizable nature. We argue that this offset can be problematic in concurrent EEG recordings, as they pose the risk of amplifier saturation and distortions of the recorded stimulation waveform.

neuroscience↗

bioRxiv2024

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt for two consecutive years, 2022 and 2023, from 22 countries in Europe and surrounding regions, and compiled a genomic dataset of 415 Bgt isolates. We found one single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.

evolutionary biology↗

bioRxiv2024

Photochromic reversion enables long-term tracking of single molecules in living plants.

Single-molecule imaging enables the observation of individual molecules in living cells (DEste et al., 2024; Kusumi et al., 2014; Lelek et al., 2021; Nguyen et al., 2023). In plants, however, the tracking of single molecules is typically limited to a few hundred milliseconds (Bayle et al., 2021; Gronnier et al., 2017; Hosy et al., 2015), precluding the observation of dynamic cellular processes at molecular resolution. Here, we describe photochromic reversion, an imaging modality that enables long-term single-molecule tracking of genetically encoded translational fusions. Using this approach, we achieve minute-long tracking of individual cell-surface receptors and reveal previously inaccessible dynamic spatial arrest events of single plasma membrane proteins. We further developed and benchmarked computational analysis of spatial arrests (CASTA), a machine learning-based tool that automatically detects and analyses spatial, temporal, and diffusional properties of these events, thereby enabling precise nanoscale kinetic measurements. Together, these advances provide a powerful framework for deciphering the principles governing membrane dynamics and function.

cell biology↗

bioRxiv2023

Imaging of plant calcium-sensor kinase conformation monitors real time calcium decoding in planta

Changes in cytosolic calcium concentration are among the earliest reactions to a multitude of stress cues. Whereas a plethora of calcium-permeable channels may generate distinct calcium signatures and contribute to response specificities, the mechanisms by which calcium signatures are decoded is poorly understood. Here we develop a genetically encoded, FRET-based reporter that visualizes the conformational change of calcium-dependent protein kinases (CDPKs/CPKs), preceding kinase activation, for calcium-dependent AtCPK21 and calcium-independent AtCPK23. In pollen tubes, naturally displaying a physiological calcium range, CPK21-FRET, but not CPK23-FRET, report activity oscillations with similar features to cytosolic calcium, suggesting an isoform-specific calcium dependency and reversibility of the conformational change. In guard cells CPK21-FRET identifies CPK21 as a decoder of signal-specific calcium signatures in response to ABA and flg22. Based on this data, CDPK-FRET stands as a novel approach for tackling real-time live-cell calcium decoding in a multitude of plant developmental and stress responses.

biochemistry↗

bioRxiv2021

A chemerin peptide analog stimulates tumor growth in two xenograft mouse models of human colorectal carcinoma

BackgroundChemerin plasma concentration has been reported to be positively correlated with the risk of colorectal cancer. However, the potential regulation of CRC tumorigenesis and progression has not yet been investigated in an experimental setting. This study addresses this hypothesis by investigating proliferation, colony formation and migration of CRC cell lines in vitro as well as in animal models. MethodsIn vitro, microscopic assays to study proliferation as well as a scratch-wound assay for migration monitoring were applied using the human CRC cell lines HCT116, HT29 and SW620 under the influence of the chemerin analog CG34. The animal study investigated HCT116-luc and HT29-luc subcutaneous tumor size and bioluminescence during treatment with CG34 versus control, followed by ex-vivo analysis of vessel density and mitotic activity. ResultsWhile proliferation of the three CRC cell lines in monolayers was not clearly stimulated by CG34, the chemerin analog promoted colony formation in three-dimensional aggregates. An effect on cell migration was not observed. In the treatment study, CG34 significantly stimulated both growth and bioluminescence signal of HCT116-luc and HT29-luc xenografts. ConclusionsThe results of this study represent the first indication of a tumor growth-stimulating effect of chemerin signaling in CRC.

cancer biology↗