Biology subjects

Krueger, T.

Publications and source records attributed to Krueger, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Dissociating Resting-State Networks of Pedohebephilic Preference and Child Sexual Offending Using Network-Based Prediction

Background: Pedohebephilia (P+), the sexual preference for prepubescent and early pubertal minors, regularly causes distress in those affected. While associated with child sexual offending (CSO), P+ is not a prerequisite for CSO. Limited neuroimaging studies have identified alterations associated with P+, while these may primarily reflect offending history. The correlates of P+ independent of CSO therefore remain unclear. We examined this distinction using intrinsic functional networks within a multivariate predictive framework. Methods: Using resting-state functional connectivity (rsFC) and network-based prediction (NBS-Predict), we performed pairwise classifications among non-offending pedohebephilic men (P+CSO-, n=35), pedohebephilic men with CSO (P+CSO+, n=38), and non-pedohebephilic controls without CSO (P-CSO-, n=63). Classification-relevant subnetwork nodal strength was associated post hoc with trait impulsivity within P+ groups. Results: P+CSO- were significantly distinguished from P-CSO- (balanced accuracy [BAC]=0.621, pFDR=.041), and showed reductions between default-mode hubs and temporoparietal somatomotor and ventral attention regions. P+CSO+ were also significantly distinguished from P+CSO- (BAC=0.645, pFDR=.032) and yielded a smaller subnetwork centered on the substantia nigra. Against P-CSO-, P+CSO+ showed widespread reductions, particularly across subcortical, default mode, visual, limbic, and somatomotor regions (BAC=0.640, pFDR=0.032). Right precentral gyrus nodal strength correlated with impulsivity in P+CSO+ only (r=0.57, pFDR=0.024). Conclusions: Whole-brain rsFC contains information distinguishing pedohebephilic preference in the absence of known CSO, while P+CSO+ show additional and more widespread network alterations involving systems implicated in action selection and behavioral regulation. These findings open new avenues for integrating pedohebephilia into broader neurobiological research frameworks.

neuroscience↗

bioRxiv2026

Cell-specific heteroclinic orbits govern interaction dynamics in inertial microfluidics for circulating tumour cell separation

Cancer survival rates increase with earlier diagnosis. However, many cancers are diagnosed only after symptoms develop, in the later stages of cancer progression. We need a diagnostic tool that can detect cancer earlier. Circulating tumour cells (CTCs) are cells that detach from the main tumour and can enter the bloodstream. The capture and analysis of CTCs can provide an early indicator of cancer. However, rarity of CTCs in blood makes their efficient capture challenging. Inertial microfluidics can be utilised for a label-free separation of CTCs from white blood cells (WBCs) by manipulating cells in the microchannel based on cell properties, achieving good separation performance. Inertial microfluidic devices mainly rely on size-based separation. However, residual WBC carryover limits complete separation. Here, we show that cell mechanical heterogeneity plays a large role in the separation process and should be considered in the design of these devices. We simulate the migration dynamics of CTCs and WBCs in a straight microchannel using a 3D lattice-Boltzmann-immersed-boundary-finite-element solver. Our results demonstrate that WBC migration behaviour changes depending on the deformability of a CTC. The size and deformability of the cells have been shown to determine the cell-specific heteroclinic orbits leading to different interaction types, these interactions alter WBC migration resulting in more/less WBC carryover. This work highlights that both cell-specific heteroclinic orbits and single cell migration rates should be considered in the design of inertial microfluidics for separation.

bioengineering↗

bioRxiv2026

Candida glabrata YPK2 is a multidrug susceptibility locus

The biological conservation between fungi and mammals due to a common ancestor has made development of selective antifungal drugs a difficult challenge. Further complicating this situation is the selection of antifungal drug-resistant organisms during drug treatment. The pathogenic yeast Nakaseomyces glabratus (called here Candida glabrata) presents an especially challenging organism due to its tendency to frequently lose susceptibility to the major antifungal drug class the azoles. Additionally, C. glabrata develops resistance to echinocandin drugs, a second, more recently described antifungal agent at 10 times the rate of other organisms. Previous work has established that the sterol responsive transcriptional regulator Upc2A is a key determinant of azole susceptibility in C. glabrata and plays a role in echinocandin resistance. We used a biochemical approach to identify proteins that co-purified with Upc2A and identified the Ypk2 AGC kinase as an interacting protein. Strains lacking YPK2 exhibited increased susceptibility to fluconazole and the echinocandin caspofungin. A ypk2{Delta} strain failed to normally induce transcription of several ERG genes but exhibited normal induction of the CDR1 ATP-binding cassette transporter gene. Isogenic ypk2{Delta} strains were also highly susceptible to the three major classes of antifungal drugs, indicating that this kinase behaves as a multidrug susceptibility factor. RNA-seq analyses indicated that the transcriptional response to exposure is different for each drug and each response is differentially altered upon loss of Ypk2. Our data indicate that Ypk2 plays an important role in coordinating gene expression that impacts susceptibility to all major antifungal drug classes.

molecular biology↗

bioRxiv2025

Numerical study of the size-based, shear-induced separation ofcirculating tumour cells from white blood cells in liquid biopsies

Circulating tumour cells (CTCs) are promising biomarkers for early cancer detection, yet their extreme rarity in blood necessitates efficient separation from white blood cells (WBCs) in lysed liquid biopsies. Inertial microfluidics offers a high-throughput, label-free approach to this challenge by leveraging size-dependent lateral migration. However, experimental observations reveal that WBCs migrate more rapidly than predicted, reducing separation performance. Using 3D lattice-Boltzmann-immersed-boundary-finite-element simulations, we characterized the migration dynamics of CTCs and WBCs in a straight microchannel. Our results reveal that the presence of a CTC enhances WBC cross-streamline migration, providing a mechanistic explanation for WBC contamination in CTC-enriched outlets. The numerical model capturing heterochiral orbital dynamics was validated experimentally, confirming the role of intercellular hydrodynamic interactions. These findings underscore the critical role of intercellular interactions in inertial microfluidic systems and provide guidance for optimizing suspension concentration and channel geometry to improve purity in rare cell isolation.

bioengineering↗

bioRxiv2025

Exo-Tox: Identifying Exotoxins from secreted bacterial proteins

BackgroundBacterial exotoxins are secreted proteins able to affect target cells, and associated with diseases. Their accurate identification can enhance drug discovery and ensure the safety of bacteria-based medical applications. However, current toxin predictors prioritize broad coverage by mixing toxins from multiple biological kingdoms and diverse control sets. This general approach has proven sub-optimal for identifying niche toxins, such as bacterial exotoxins. Recent Protein Language Models offer an opportunity to improve toxin prediction by capturing global sequence context and biochemical properties from protein sequences. ResultsWe introduce Exo-Tox, a specialized predictor trained exclusively on curated datasets of bacterial exotoxins and secreted non-toxic bacterial proteins, represented as embeddings by Protein Language Models. Compared to Basic Local Alignment Search Tool (BLAST)-based methods and generalized toxin predictors, Exo-Tox outperforms across multiple metrics, achieving an Matthews correlation coefficient > 0.9. Notably, Exo-Toxs performance remains robust regardless of protein length or the presence of signal peptides. We analyze its limited transfer-ability to bacteriophage proteins and non-secreted proteins. ConclusionExo-Tox reliably identifies bacterial exotoxins, filling a niche overlooked by generalized predictors. Our findings highlight the importance of domain-specific training data and emphasize that specialized predictors are necessary for accurate classification. We provide open access to the model, training data, and usage guidelines via the LMU Munich Open Data repository.

bioinformatics↗

bioRxiv2025

Suspension physics govern the multiscale dynamics of blood flow in sickle cell disease

In diseases from diabetes to malaria, blood dynamics are significantly altered, resulting in poor clinical outcomes. However, the multiscale mechanisms that determine blood flow in the microcirculation in health and disease are undefined, largely owing to the difficulty in directly linking cell properties to whole-blood rheology. Here, we overcome these difficulties by developing a microfluidic platform to measure red blood cell properties and flow dynamics in the same blood samples from donors. We focus on sickle cell disease (SCD), a genetic disorder that causes red blood cells to stiffen in deoxygenated conditions, with disease pathology driven by oxygen-dependent blood rheology. Our linked cell and whole-blood measurements establish that increases in effective resistances in heterogeneous suspensions are driven by increases in the proportion of stiff cells, similar macroscopically to the behavior of rigid-particle suspensions. Furthermore, by combining simulations with spatially resolved measurements of cell dynamics, we show how the spatio-temporal organization of stiff and deformable cells determines blood rheology and drives disease pathophysiology. In the presence of deformable cells, the stiffened cells marginate towards channel walls, increasing effective wall friction. In fully deoxygenated conditions in which all cells are stiffened, significant heterogeneity in cell volume fraction along the direction of flow causes localized jamming, drastically increasing effective viscous flow resistance. Our work defines the relevant suspension physics required to understand pathological blood rheology in SCD and other diseases affecting red blood cell properties. More broadly, we reveal the multiscale processes that determine emergent rheology in heterogeneous particle suspensions.

physiology↗

bioRxiv2024

Abnormal vasculature reduces overlap between drugs and oxygen in a tumour computational model: implications for therapeutic efficacy

The tumour microvasculature is abnormal, and as a consequence oxygen and drug transport to the tumour tissue is impaired. The abnormal microvasculature contributes to tumour tissue hypoxia, as well as to varying drug penetration depth in the tumour. Many anti-cancer treatments require the presence of oxygen to be fully efficacious, however the question of how well oxygen concentration overlaps with drug concentration is not elucidated, which could compromise the therapeutic effect of these drugs. In this work we use a computational model of blood flow and oxygen transport, and develop a model for an oxygen-dependent drug, T-DM1, to study the overlap of oxygen and drug concentration in healthy and tumour tissue, where we assume the tumour tissue to compress blood vessels. Our results show that, due to the compressed vessels present in tumours, areas of sufficient oxygen concentration for a drug to function overlap poorly with areas of sufficient drug concentration, covering 28% of the tumour tissue, compared to 82% in healthy tissue. The reduction in drug and oxygen overlap is due to the altered red blood cell dynamics through the abnormal microvasculature, and indicates that drug transport to tumours should not be considered independently of oxygen transport in cases where the drug requires oxygen to function.

biophysics↗

bioRxiv2024

Modelling trypanosome motility

African trypanosomiasis, or sleeping sickness, is a life-threatening disease caused by the protozoan parasite Trypanosoma brucei. The bloodstream form of T. brucei has a slender body with a relatively long active flagellum, which makes it an excellent swimmer. We develop a realistic trypanosome model and perform mesoscale hydrodynamic simulations to study the importance of various mechanical characteristics for trypanosome swimming behavior. The cell body is represented by an elastic triangulated network, while the attached flagellum consists of four interconnected running-in-parallel filaments, which permits a good control of the flagellum beating plane. Our simulation results are validated against experimental observations, and highlight the crucial role of body elasticity, non-uniform actuation along the flagellum length, and the orientation of flagellum-beating plane with respect to the body surface for trypanosome locomotion. These results offer a framework for exploring parasite behavior in complex environments.

biophysics↗

bioRxiv2024

DOG1 prevents AFPs activation by AHG1 to control dormancy separately from ABA core signaling

Seed dormancy determines germination timing and thereby critically influences seed plant adaptation and overall fitness. DELAY OF GERMINATION1 (DOG1) is a conserved central regulator of dormancy acting in concert with the phytohormone abscisic acid (ABA) through negative regulation of ABA HYPERSENSITIVE GERMINATION (AHG) 1 and AHG3 phosphatases. The current molecular mechanism of DOG1 signaling proposes that it regulates the activation state of central ABA-related SnRK2 kinases. Here, we unveil DOG1s functional autonomy from the regulation of ABA core signaling components and unravel its pivotal control over the activation of ABSCISIC ACID INSENSITIVE FIVE BINDING PROTEINs (AFPs). Our data revealed a DOG1-AHG1-AFP relay in which AFPs genuine activation by AHG1 is contained by DOG1 to prevent the breakdown of maturation-imposed ABA responses independently of ABA-related kinase activation status. This work offers a molecular understanding of how plants fine-tune germination timing, while preserving seed responsiveness to adverse environmental cues, and thus represents a milestone in the realm of conservation and breeding programs. One-Sentence SummaryAutonomous control of maturation-imposed ABA responses by DOG1 enables seeds to regulate dormancy and stress-reactivity traits independently.

plant biology↗

bioRxiv2024

Quantification of Trypanosoma Brucei social motilityindicates different colony growth phases

In vitro colonies of the flagellated parasite Trypanosoma brucei grow in characteristic fingering instability patterns. The underlying cause of this this type of collective migration and the associated behavior called social motility remains a topic of intense debate in the scientific community. In order to study these mechanisms in detail, it is crucial to develop quantitative methods to assess and measure social motility patterns at the level of the whole colony beyond qualitative image comparisons. Here, we show a quantification of the growth process based on two scale free metrics designed to quantify the shape of two-dimensional colonies. While initially developed for yeast colonies, we adapted, modified and extended the analysis pipeline for the Trypanosoma system. Combining the quantitative measurements with colony growth simulations based on the Eden model, we discovered two distinct growth phases in social motility showing colonies: In the first phase, the colonies shown mainly circular expansion and later switch to an almost exclusive finger growing phase. These phases are robust when increasing the number of cells as well as upon partial inhibition of the finger formation. A newly developed anisotropy index shows that upon partial inhibition the anisotropy in the colony increases over time. Our results provide objective measurements that help advance the understanding of social motility of trypanosomes. Furthermore, our approach is suitable as a blueprint for investigations of other colony forming cells such as yeast or bacteria.

biophysics↗

bioRxiv2024

Patient-derived lymphomoids preserve the tumor architecture and allow to assess response to therapies in lymphoma

The efficacy of anti-cancer therapies depends on the genomic composition of the tumor, its microenvironment, spatial organization, and intra-tumor heterogeneity. B cell lymphomas are a heterogeneous group of tumors emerging from B cells at different stages of differentiation and exhibiting tumor-specific interactions with the tumor microenvironment. Thus, to measure response to therapy in lymphoma, it is critical to preserve the tumor composition and functional interactions among immune cells. Here, we developed a platform to maintain small fragments of human lymphoma tissue in culture for several days and use them to test response to therapies. We collected 25 patient samples representative of different lymphoma subtypes and established ex vivo tissue fragments that retained histological, cellular, and molecular characteristics of the original tissue, here referred to as lymphomoids. Using lymphomoids, we tested sensitivity to several clinically approved small molecule inhibitors in parallel and examined tissue remodeling upon treatment. Importantly, when this information was available, we showed that sensitivity to therapy observed in lymphomoids was consistent with patients response in the clinic. Lymphomoids are an innovative tool to assess treatment efficacy in clinically relevant contexts and could be used to uncover novel aspects of lymphoma biology.

cancer biology↗

bioRxiv2024

Mod5 mediates a molecular trade-off between optimal gene expression and antifungal resistance.

Increasing antifungal drug resistance is a major concern associated with human fungal pathogens like Aspergillus fumigatus. Genetic mutation and epimutation mechanisms clearly drive resistance, yet the epitranscriptome remains relatively untested. Here, deletion of the A. fumigatus tRNA-modifying isopentenyl transferase ortholog, Mod5, led to altered stress response and unexpected resistance against the antifungal drug 5-fluorocytosine (5-FC). After confirming the canonical isopentenylation activity of Mod5 by LC-MS/MS and Nano-tRNAseq, we performed simultaneous profiling of transcriptomes and proteomes to reveal a comparable overall response to 5-FC stress; however, a premature activation of cross-pathway control (CPC) genes in the knockout was further increased after antifungal treatment. We identified several orthologues of the A. nidulans Major Facilitator Superfamily (MFS) transporter nmeA as specific CPC-client genes in A. fumigatus. Overexpression of Mod5-target tRNATyrG{Psi}A in the {Delta}mod5 strain rescued select phenotypes but failed to reverse 5-FC resistance, whereas deletion of nmeA largely, but incompletely, reverted the resistance phenotype, implying additional relevant exporters. In conclusion, 5-FC resistance in the absence of Mod5 and i6A likely originates from multifaceted transcriptional and translational changes that skew the fungus towards premature CPC-dependent activation of antifungal toxic-intermediate exporter nmeA, offering a potential mechanism reliant on RNA modification to facilitate transient antifungal resistance.

microbiology↗

bioRxiv2023

Numerical investigation of heterogeneous soft particle pairs in inertial microfluidics

The formation of pairs of particles or cells of different types in microfluidic channels can be desired or detrimental in healthcare applications. It is still unclear what role softness heterogeneity plays in the formation of these particle pairs. We use an in-house lattice-Boltzmann-immersed-boundary-finite-element solver to simulate a pair of particles with different softness flowing through a straight channel with a rectangular cross-section under initial conditions representative of a dilute suspension. We find that softness heterogeneity significantly affects the pair dynamics, determining whether a pair will form or not, and determining the lateral and inter-particle equilibrium behaviour in the pair. We also observe close matches between the transient deformation of particles in a linear pair and single particles in isolation. These results further our understanding of pair behaviour, providing a foundation for understanding particle train formation, and open up the potential to develop reduced-order models for particle pair formation based upon the behaviour of single particles.

bioengineering↗

bioRxiv2023

Apical annuli are specialised sites of post-invasion secretion of dense granules in Toxoplasma

Apicomplexans are ubiquitous intracellular parasites of animals. These parasites use a programmed sequence of secretory events to find, invade, and then reengineer their host cells to enable parasite growth and proliferation. The secretory organelles micronemes and rhoptries mediate the first steps of invasion. Both secrete their contents through the apical complex which provides an apical opening in the parasites elaborate inner membrane complex (IMC) -- an extensive subpellicular system of flattened membrane cisternae and proteinaceous meshwork that otherwise limits access of the cytoplasm to the plasma membrane for material exchange with the cell exterior. After invasion, a second secretion programme drives host cell remodelling and occurs from dense granules. The site(s) of dense granule exocytosis, however, has been unknown. In Toxoplasma gondii, small subapical annular structures that are embedded in the IMC have been observed, but the role or significance of these apical annuli to plasma membrane function has also been unknown. Here, we determined that integral membrane proteins of the plasma membrane occur specifically at these apical annular sites, that these proteins include SNARE proteins, and that the apical annuli are sites of vesicle fusion and exocytosis. Specifically, we show that dense granules require these structures for the secretion of their cargo proteins. When secretion is perturbed at the apical annuli, parasite growth is strongly impaired. The apical annuli, therefore, represent a second type of IMC-embedded structure to the apical complex that is specialised for protein secretion, and reveal that in Toxoplasma there is a physical separation of the processes of pre- and post-invasion secretion that mediate host-parasite interactions.

cell biology↗

bioRxiv2023

Continuous endosomes form functional subdomains and orchestrate rapid membrane trafficking in trypanosomes

Endocytosis is a common process observed in most eukaryotic cells, although its complexity varies among different organisms. In Trypanosoma brucei, the endocytic machinery is under special selective pressure because rapid membrane recycling is essential for immune evasion. This unicellular parasite effectively removes host antibodies from its cell surface through hydrodynamic drag and fast endocytic internalization. The entire process of membrane recycling occurs exclusively through the flagellar pocket, an extracellular organelle situated at the posterior pole of the spindle-shaped cell. The high-speed dynamics of membrane flux in trypanosomes do not seem compatible with the conventional concept of distinct compartments for early, late and recycling endosomes. To investigate the underlying structural basis for the remarkably fast membrane traffic in trypanosomes, we employed advanced techniques in light and electron microscopy to examine the three-dimensional architecture of the endosomal system. Our findings reveal that the endosomal system in trypanosomes exhibits a remarkably intricate structure. Instead of being compartmentalized, it constitutes a continuous membrane system, with specific functions of the endosome segregated into membrane subdomains enriched with classical markers for early, late, and recycling endosomes. These membrane subdomains can partly overlap or are interspersed with areas that are negative for endosomal markers. This continuous endosome allows fast membrane flux by facilitated diffusion that is not slowed by multiple fission and fusion events.

cell biology↗

bioRxiv2023

Lattice-Boltzmann Modelling for Inertial Particle Microfluidics Applications -A Tutorial Review

Inertial particle microfluidics (IPMF) is an emerging technology for the manipulation and separation of microparticles and biological cells. Since the flow physics of IPMF is complex and experimental studies are often time-consuming or costly, computer simulations can offer complementary insights. In this tutorial review, we provide a guide for researchers who are exploring the potential of the lattice-Boltzmann (LB) method for simulating IPMF applications. We first review the existing literature to establish the state of the art of LB-based IPMF modelling. After summarising the physics of IPMF, we then present related methods used in LB models for IPMF and show several case studies of LB simulations for a range of IPMF scenarios. Finally, we conclude with an outlook and several proposed research directions.

biophysics↗

bioRxiv2023

Effect of vessel compression on blood flow in microvascular networks: implications for tumour tissue hypoxia

The tumour microenvironment is abnormal and one of its consequences is that blood vessels are compressed. Vessel compression correlates with reduced survival rates, while decompression of vessels improves tissue oxygenation as well as increases survival rates. Vessel compression contributes, at a single vascular bifurcation, to the increase of heterogeneity of red blood cell (RBC) transport. However, the effect that vessel compression has at a network level is unknown. This work numerically investigates the effect of vessel compression on RBC transport in microvascular networks. The key findings are that vessel compression both reduces the average haematocrit, and increases haematocrit heterogeneity, in vessels in the network. The mechanisms for these changes in haematocrit distribution are unravelled, and a parameter sweep shows that networks with lower inlet haematocrits are more susceptible to haemodilution from vessel compression over a wide range of compressed fraction of a network. These findings provide a theoretical underpinning for the link between vessel compression and tumour tissue hypoxia.

biophysics↗

bioRxiv2022

Numerical study of the formation and stability of a pair of particles of different sizes in inertial microfluidics

The formation of pairs and trains of particles in inertial microfluidics is an important consideration for device design and applications, such as particle focussing and separation. We study the formation and stability of linear and staggered pairs of nearly rigid spherical particles of different sizes in a pressure-driven flow through a straight duct with rectangular cross-section under mild inertia. An in-house lattice-Boltzmann-immersed-boundary-finite-element code is used for the simulations. We find that the stability and properties of pairs of heterogeneous particles strongly depends on the particle sizes and their size ratio, while the formation of the pairs is also determined by the initial lateral position and the axial order of the particles. Our findings imply that perturbations of particle trajectories caused by other particles, as they are expected to happen even in dilute suspensions, can be important for the formation of stable pairs in inertial microfluidics.

biophysics↗