Biology subjects

Thiele, M.

Publications and source records attributed to Thiele, M..

12 recordsLinked to original sources

bioRxiv2026

Structural Mapping of the EIN2-EIN3 Interaction Core and Its Integration with ENAP1 in Ethylene Signaling

Ethylene regulates diverse developmental processes, yet the molecular function of its central regulator, ETHYLENE INSENSITIVE 2 (EIN2), has remained unclear. Although EIN2 nuclear import is mediated by the Importin-/{beta} pathway, the molecular events initiated by EIN2 after nuclear entry were unknown. Here we show that EIN2 directly engages the transcription factor EIN3, establishing a mechanistic link between EIN2 nuclear accumulation and transcriptional activity. Microscale thermophoresis, yeast two-hybrid analysis and in planta FLIM-FRET consistently support this interaction. Domain mapping identifies EIN3 residues 86-173 as the core EIN2-binding region, and structural modeling refines the interface to a conserved segment within residues 86-120 that contacts a conserved region near the N-terminus of the EIN2-CEND fragment. In planta, EIN2 residues 1042-1214 are sufficient for EIN3 binding, revealing multiple interaction-competent surfaces with distinct affinities. The chromatin-associated protein ENAP1 also binds EIN2 and competes with EIN3, indicating a dynamic, concentration-dependent regulatory mechanism rather than a stable ternary complex. These findings define the molecular basis of the EIN2-EIN3 interaction and provide a mechanistic framework for EIN2-dependent transcriptional control in ethylene signaling.

plant biology↗

bioRxiv2026

HIV Infection in Humanized Microglial Mice Disrupts Feeding Behavior and Circadian Rhythms with Cortical Neuroinflammation

Although effective antiretroviral therapy (ART) has substantially reduced the severity of human immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND), the condition remains highly prevalent. Understanding HAND has been a challenge due to the lack of small animal models capable of supporting productive HIV infection in the brain. Recent advances in humanized mouse models with engrafted human glial cells now enable systemic HIV infection that extends to the central nervous system, offering a powerful platform to study HAND pathogenesis. In this study, we investigated behavioral alterations and neuropathological changes associated with HIV infection. Using home-cage monitoring, we observed that HIV-infected mice exhibited reduced feeding efficiency, consuming less food despite spending more time at the feeder, compared to uninfected controls. Additionally, infected animals displayed disrupted circadian rhythms, with a significant correlation between central nervous system viral load and increased locomotor activity during the light cycle. Neuropathological analyses revealed region-specific vulnerability, with the cortex exhibiting pronounced inflammatory and neurodegenerative changes. These findings were supported by transcriptomic profiling, which demonstrated heightened inflammatory and antiviral gene expression in the cortex, along with differentially expressed genes associated with neuropathology and behavioral deficits. Together, these results highlight distinct region-specific responses to HIV infection in the brain and establish this humanized mouse model as a valuable tool for elucidating the mechanisms underlying HAND and its associated behavioral deficits.

neuroscience↗

bioRxiv2025

Joint attention biases dogs' memory towards object identity

Ostensive communication, characterized by direct eye contact and other attention-catching signals, shapes how humans encode and remember novel objects, biasing memory toward identity-relevant features. Dogs are sensitive to human ostensive cues and follow gaze direction. However, whether these signals also enhance and modulate object encoding remains unknown. In an eye-tracking study, we tested dogs in a violation-of-expectation paradigm. A human actor directed eye contact toward the dog or looked away while looking at an object. After an occlusion, dogs viewed three outcomes: the same object (no change), the same object in a different location (location change), or a different object (identity change). We measured dogs looking times during the outcome phase within predefined areas of interest around the object. In line with our predictions and matching earlier findings with infants, dogs looked longer at identity changes in the eye-contact condition. In contrast, looking times at location and no-change outcomes were unaffected by communicative context, indicating selective enhancement of identity encoding. During the initial addressing phase, pupil dilation was greater in the eye-contact condition, indicating increased arousal or engagement. These findings demonstrate that dogs and infants exhibit a communication-induced memory bias, revealing a capacity for ostension-guided learning that facilitates information transfer.

animal behavior and cognition↗

bioRxiv2025

Integration of auxin and cytokinin signalling in Arabidopsis root meristem maintenance through the secreted peptide CLE40

Plant meristems perpetually generate new cells for the initiation, growth and differentiation of various cell types and organs. CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) genes encode plant specific peptides exerting indispensable functions in a multitude of these developmental processes. Previously, we have described a CLE40 signaling module that regulates stemness in the distal root meristem (DRM). Here, we show that CLE40 is additionally needed to maintain the proximal root meristem (PRM). We demonstrate that in cle40 mutants, meristematic cells differentiate prematurely, resulting in shortened PRMs and ultimately, reduced root growth. Furthermore, we link these effects to increased cytokinin signaling that can be circumvented by preventing the perception of cytokinin. We highlight how increased cytokinin signaling leads to a change in auxin distribution mediated by SHORT HYPOCOTYL 2 (SHY2), which is ectopically activated if CLE40 is not active. Finally, we propose that the receptor BARELY ANY MERISTEM 1 (BAM1), but not its homolog BAM2, perceives CLE40 in the PRM.

developmental biology↗

bioRxiv2024

Cyclical MinD membrane affinity differences are not necessary for MinD gradient formation in Bacillus subtilis

Proteins can diffuse micrometers in seconds, yet bacterial cells are able to maintain stable protein gradients. The best studied bacterial protein gradient is the Min system of Escherichia coli. In rod-shaped bacteria the MinCD proteins prevent formation of minicells by inhibiting FtsZ polymerization close to the cell poles. In E. coli these proteins oscillate between cell poles within a minute, resulting in an increased MinCD concentration at the poles. This oscillation is caused by the interaction between MinD and the protein MinE, which form an ATP-driven reaction-diffusion system, whereby the ATPase MinD cycles between a monomeric cytosolic and a dimeric membrane attached states. Bacillus subtilis also has MinCD, but lacks MinE. In this case MinCD form a static gradient that requires the transmembrane protein MinJ, located at cell poles and cell division sites. A recent reaction-diffusion model was successful in recreating the MinD gradient in B. subtilis, assuming that MinD cycles between cytosol and membrane, like in E. coli. Here we show that the monomeric and dimeric states of B. subtilis MinD have comparable membrane affinities, that MinD interacts with MinJ as a dimer, and that MinJ is not required for membrane localization of MinD. Based on these new findings we tested different models, using kinetic Monte Carlo simulations, and found that a difference in diffusion rate between the monomer and dimer, rather than a difference in membrane affinity, is important for B. subtilis MinCD gradient formation.

microbiology↗

bioRxiv2024

Working memory enhancement using real-time phase-tuned transcranial alternating current stimulation

BackgroundPrior work has shown that transcranial alternating current stimulation (tACS) of parietooccipital alpha oscillations (8 - 14 Hz) can modulate working memory (WM) performance as a function of the phase lag to endogenous oscillations. However, leveraging this effect using real-time phase-tuned tACS was not feasible so far due to stimulation artifacts. Objectives/HypothesisWe aimed to develop a system that tracks and adapts the phase lag between tACS and ongoing parietooccipital alpha oscillations in real-time. We hypothesized that such real-time phase-tuned tACS enhances working memory performance, depending on the phase lag. MethodsWe developed real-time phase-tuned closed-loop amplitude-modulated tACS (CLAM-tACS) targeting parietooccipital alpha oscillations. CLAM-tACS was applied at six different phase lags relative to ongoing alpha oscillations while participants (N = 21) performed a working memory task. To exclude that behavioral effects of CLAM-tACS were mediated by other factors such as sensory co-stimulation, a second group of participants (N = 25) received equivalent stimulation of the forehead. ResultsWM accuracy improved in a phase lag dependent manner (p < 0.05) in the group receiving parietooccipital stimulation, with the strongest enhancement observed at 330{degrees} phase lag between tACS and ongoing alpha oscillations (p < 0.01, d = 0.976). Moreover, across participants, modulation of frontoparietal alpha oscillations correlated both in amplitude (p < 0.05) and phase (p < 0.05) with the modulation of WM accuracy. No such effects were observed in the control group receiving frontal stimulation. ConclusionsOur results demonstrate the feasibility and efficacy of real-time phase-tuned CLAM-tACS in modulating both brain activity and behavior, thereby paving the way for further investigation into brain-behavior relationships and the exploration of innovative therapeutic applications.

neuroscience↗

bioRxiv2023

Hydrogels with stiffness-degradation spatial patterns control anisotropic 3D cell response

In nature, tissues are patterned, but most biomaterials used in human applications are not. Patterned biomaterials offer the opportunity to mimic spatially segregating biophysical and biochemical properties found in nature. Engineering such properties allows to study cell-matrix interactions in anisotropic matrices in great detail. Here, we developed alginate-based hydrogels with patterns in stiffness and degradation, composed of distinct areas of soft non-degradable (Soft-NoDeg) and stiff degradable (Stiff-Deg) material properties. The hydrogels exhibit emerging patterns in stiffness and degradability over time, taking advantage of dual Diels-Alder covalent crosslinking and UV-mediated peptide crosslinking. The materials were mechanically characterized using rheology for single-phase and surface micro-indentation for patterned materials. 3D encapsulated mouse embryonic fibroblasts (MEFs) allowed to characterize the anisotropic cell-matrix interaction in terms of cell morphology by employing a novel image-based quantification tool. Live/dead staining showed no differences in cell viability but distinct patterns in proliferation, with higher cell number in Stiff-Deg materials at day 14. Patterns of projected cell area became visible already at day 1, with larger values in Soft-NoDeg materials. This was inverted at day 14, when larger projected cell areas were identified in Stiff-Deg. This shift was accompanied by a significant decrease in cell circularity in Stiff-Deg. The control of anisotropic cell morphology by the material patterns was also confirmed by a significant increase in filopodia number and length in Stiff-Deg materials. The novel image-based quantification tool was useful to spatially visualize and quantify the anisotropic cell response in 3D hydrogels with stiffness-degradation spatial patterns. Our results show that patterning of stiffness and degradability allows to control cell anisotropic response in 3D and can be quantified by image-based strategies. This allows a deeper understanding of cell-matrix interactions in a multicomponent material.

bioengineering↗

bioRxiv2021

High-throughput UHPLC-MS to screen metabolites in feces for gut metabolic health

(1) BackgroundFeces are the product of our diets and have been linked to diseases of the gut, including Chrons disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical methods that maximize metabolite detection. (2) MethodsAs sample preparation is crucial to obtain high quality data in MS-based clinical metabolomics, we developed a novel, efficient and robust method for preparing fecal samples for analysis with a focus in reducing aliquoting and detecting both polar and non-polar metabolites. Fecal samples (n= 475) from patients with alcohol-related liver disease and healthy controls were prepared according to the proposed method and analyzed in an UHPLC-QQQ targeted platform in order to obtain a quantitative profile of compounds that impact liver-gut axis metabolism. (3) ResultsMS analyses of the prepared fecal samples have shown reproducibility and coverage of n=28 metabolites, mostly comprising bile acids and amino acids. We report metabolite-wise relative standard deviation (RSD) in quality control samples, inter-day repeatability, LOD, LOQ and range of linearity. The average concen-trations for 135 healthy participants are reported here for clinical applications. (4) Conclusionsour high-throughput method provides an efficient tool for investigating gut-liver axis metabolism in liver-related diseases using a noninvasive collected sample.

biochemistry↗

bioRxiv2021

Fungi hijack a plant apoplastic endoglucanase to release a ROS scavenging β-glucan decasaccharide to subvert immune responses

Plant pathogenic and beneficial fungi have evolved several strategies to evade immunity and cope with host-derived hydrolytic enzymes and oxidative stress in the apoplast, the extracellular space of plant tissues. Fungal hyphae are surrounded by an inner, insoluble cell wall (CW) layer and an outer, soluble extracellular polysaccharide (EPS) matrix. Here we show by proteomics and glycomics that these two layers have distinct protein and carbohydrate signatures, implicating different biological functions. The barley (Hordeum vulgare) {beta}-1,3-endoglucanase HvBGLUII, which belongs to the widely distributed apoplastic glycoside hydrolase 17 family (GH17), releases a conserved {beta}-1,3;1,6-glucan decasaccharide ({beta}-GD) from the EPS matrices of fungi with different lifestyles and taxonomic positions. This low molecular weight {beta}-GD does not activate plant immunity, is resilient to further enzymatic hydrolysis by {beta}-1,3-endoglucanases due to the presence of three {beta}-1,6-linked glucose branches and can scavenge reactive oxygen species. Additionally, exogenous application of {beta}-GD leads to enhanced fungal colonization in barley. Our data highlights the hitherto undescribed capacity of this often overseen fungal EPS layer to act as an outer protective barrier important for fungal accommodation within the hostile environment at the apoplastic plant-microbe interface. SignificanceHere we identify and characterize a conserved {beta}-1,3;1,6-glucan decasaccharide with antioxidant activity released from the fungal extracellular polysaccharide (EPS) matrix by the activity of a plant apoplastic endoglucanase. In addition, we provide a quantitative proteomic analysis of the fungal EPS and cell wall (CW) layers. HIGHLIGHTSO_LIThe fungal extracellular polysaccharide (EPS) matrix and the cell wall (CW) are specific layers with distinct protein and carbohydrate signatures C_LIO_LIA conserved {beta}-1,3;1,6-glucan decasaccharide ({beta}-GD) is released from the EPS matrices of different fungi by the activity of the barley {beta}-1,3-endoglucanase BGLUII, a member of the widely distributed apoplastic GH17 family C_LIO_LIThe {beta}-GD efficiently scavenges reactive oxygen species (ROS) and enhances fungal colonization C_LIO_LIThe immunomodulatory potential as microbe-associated molecular pattern (MAMP) as well as the biochemical activity as ROS scavenger of soluble low molecular weight {beta}-glucans are defined by the presence of {beta}-1,6-glucose branches C_LI

microbiology↗

bioRxiv2020

A paired liver biopsy and plasma proteomics study reveals circulating biomarkers for alcohol-related liver disease

Existing tests for detecting liver fibrosis, inflammation and steatosis, three stages of liver disease that are still reversible are severely hampered by limited accuracy or invasive nature. Here, we present a paired liver-plasma proteomics approach to infer molecular pathophysiology and to identify biomarkers in a cross-sectional alcohol-related liver disease cohort of nearly 600 individuals. Metabolic functions were downregulated whereas fibrosis-associated signaling and novel immune responses were upregulated, but only half of tissue proteome changes were transmitted to the circulation. Machine learning models based on our biomarker panels outperformed existing tests, laying the foundation for a generic proteomic liver health assessment.

biochemistry↗

bioRxiv2020

Male linked genomic regions determine sex in dioecious Amaranthus palmeri

Dioecy, the separation of reproductive organs on different individuals, has evolved repeatedly in different plant families. Several evolutionary paths to dioecy have been suggested, but the mechanisms behind sex determination is not well understood. The diploid dioecious Amaranthus palmeri represents a well suited model system to study sex determination in plants. A. palmeri is one of the most troublesome weeds in the US, has successfully colonized other regions in the world and has evolved resistance to several herbicide classes. Despite the agricultural importance of the species, the genetic control and evolutionary state of dioecy in A. palmeri is currently unknown. Early cytogenetic experiments did not identify heteromorphic chromosomes. Here, we used whole genome sequencing of male and female pools from two independent populations to elucidate the genetic control of dioecy in A. palmeri. Read alignment to a close monoecious relative and allele frequency comparisons between male and female pools did not reveal significant sex linked genes. Consequently, we employed an alignment free k-mer comparison which enabled us to identify a large number of male specific k-mers. We assembled male specific contigs comprising a total of almost 2 Mb sequence, proposing a XY sex determination system in the species. Based on our findings we suggest an intermediate evolutionary state of dioecy in A. palmeri. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.

plant biology↗

bioRxiv2019

Describing the fecal metabolome in cryogenically collected samples from healthy participants.

IntroductionThe chemical composition of feces plays an important role in human metabolism. Metabolomics and lipidomics are valuable tools for screening the metabolite composition in feces. Here we set out to describe fecal metabolite composition in healthy participants in frozen stools.\n\nMethodsFrozen stool samples were collected from 10 healthy volunteers and cryogenically drilled in four areas along the specimen. Polar metabolites were analyzed using derivatization followed by two-dimensional gas chromatography and time of flight mass spectrometry. Lipids were detected using ultra high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry. The technical variation threshold was set to 30% in pooled quality control samples and metabolite variation was then assessed in four areas per specimen. A data-generated network using metabolites found in all areas was computed for healthy participants.\n\nResults2326 metabolic features were detected. Out of a total of 298 metabolites that were annotated we report here 185 that showed a technical variation of x< 30%. These metabolites included amino acids, fatty acid derivatives, carboxylic acids and phenolic compounds. Lipids predominantly belonged to the groups of diacylglycerols, triacylglycerols and ceramides. Metabolites varied between sampling areas (14%-80%). A network using metabolites present in all areas showed two main clusters, DAG lipids and phenyllactic acid.\n\nConclusionsIn feces from healthy participants, the main groups detected were phenolic compounds, ceramides, diacylglycerols and triacylglycerols. Metabolite levels differed considerably depending on the sampling area.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=52 SRC=\"FIGDIR/small/708685v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@17db665org.highwire.dtl.DTLVardef@51e140org.highwire.dtl.DTLVardef@19b55d7org.highwire.dtl.DTLVardef@120d399_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗