Biology subjects

Gottschalk, M.

Publications and source records attributed to Gottschalk, M..

11 recordsLinked to original sources

bioRxiv2026

A harmonized phantom MRI quality control framework identifies sources of longitudinal and multi-site variability

The shift towards open science in preclinical research requires high-quality, comparable data adhering to FAIR principles, yet rigorous quality assurance (QA) and quality control (QC) frameworks remain less established in preclinical magnetic resonance imaging (MRI) than in clinical imaging. To address this limitation, a multicenter study was conducted across 21 international laboratories using standardized commercial liquid phantoms for mouse and rat MRI setups and a harmonized acquisition protocol. Data processing was centralized using AIDAqc, an automated pipeline extracting quantitative metrics including signal-to-noise ratio (SNR), temporal SNR (tSNR), ghost-to-signal ratio (GSR), and motion-equivalent temporal instability, combined with five complementary outlier-detection algorithms. The evaluated datasets encompassed magnetic field strengths from 3.0 to 16.4 T and heterogeneous coil and acquisition configurations. In mouse phantom data, SNR and tSNR were significantly lower at 3 T than at 7 and 9.4 T, whereas artifact-related metrics did not differ significantly between field-strength groups. In rat phantom data, differences between field strengths were less pronounced. At 7 T, substantial dataset-specific differences were observed in anatomical and functional quality metrics, also among datasets using the similar coil configuration. Multicenter reference values for frequently represented 7 T configurations were established, including SNR/tSNR of 48 {+/-} 3/48 {+/-} 1 dB for mouse surface-coil datasets and 49 {+/-} 3/44 {+/-} 4 dB for rat array-coil datasets. Longitudinal anatomical SNR showed generally low variability, whereas ghosting was more variable across time. Automated outlier detection additionally identified transient acquisition instabilities that were not always apparent by visual inspection. Together, these findings show that field strength and nominal coil configuration alone do not adequately characterize MRI performance and support standardized, longitudinal phantom-based QC combined with automated analysis as a practical approach for improving the reliability, transparency, and interoperability of multicenter preclinical MRI data.

bioengineering↗

bioRxiv2026

Downregulation of Satb1 is required to prevent autoimmunity by maintaining Tfh homeostasis

T follicular helper (Tfh) cells are a specialized subset of CD4 T cells that localize to germinal centers (GC), where they provide critical help to B cells through the delivery of IL-21 and other cytokines. Here, we demonstrate that the tight control of the chromatin remodeler Special AT-rich sequence-binding protein 1 (Satb1) is key for this process, as overexpression of Satb1 drives lymphoproliferation and expansion of the T cell and B cell compartments in secondary lymphoid organs. Specifically, Satb1 overexpression induces a pronounced shift towards Tfh cell differentiation and increased GC formation accompanied by an increase in non-classed switched GC B cells and auto-antibody secretion. These findings highlight the importance of the precise regulation of Satb1 in fine-tuning CD4 T cells and B cells responses and suggest a potential role for dysregulation of Satb1 in the pathogenesis of autoimmune disease such as systemic lupus erythematodes (SLE).

immunology↗

bioRxiv2025

Restriction-weighted q-space trajectory imaging (ResQ): Toward mapping diffusion time effects with tensor-valued diffusion encoding in human prostate cancer xenografts

PurposeTensor-valued diffusion encoding employs gradient waveforms that enable unique sensitivity to microstructural features of tissue, but the interpretation of signal and parameters may be confounded by diffusion-time dependence. We introduce a framework for restriction-weighted q-space trajectory imaging (ResQ) that incorporates diffusion-time effects via the restriction-weighting tensor, and we evaluate it in a longitudinal study of prostate cancer xenografts treated by external radiotherapy. MethodsWe proposed a novel gradient waveform design for tensor-valued encoding with controlled restriction weighting and applied a set of four waveforms at a 9.4 T preclinical MRI system. Mice were inoculated with human prostate cancer cells (LNCaP) and assigned to groups that were untreated controls or treated by external beam irradiation. ResQ produced parameters that describes the diffusion process in terms of the mean diffusivity (D), isotropic diffusional variance (VDi), and microscopic diffusion anisotropy (VDa) as well as their diffusion-time dependence ({Delta}D, {Delta}VDi, {Delta}VDa). Analyses were performed to characterize parameters longitudinally and across groups. To highlight the consequences of ignoring restriction effects, we compared ResQ to analogous parameters estimated by q-space trajectory imaging (QTI). ResultsResQ revealed clear diffusion-time dependence across all tumors, with significant longitudinal differences between treated and untreated groups, most prominent in D, {Delta}D, and VDi. The ResQ signal representation captured the signal dynamics, whereas QTI did not. Neglecting diffusion-time dependence in QTI led to substantial parameter bias, most notably a pronounced overestimation of microscopic diffusion anisotropy. ConclusionDiffusion-time effects are non-negligible in prostate cancer and must be considered when using tensor-valued diffusion encoding. The ResQ framework enables controlled restriction weighting and improved interpretability of diffusion MRI parameters compared to approaches that ignore the effects of restriction. This provides a more principled approach for tensor-valued diffusion encoding and may enable novel imaging biomarkers that disentangle diffusivity, isotropic diffusional variance, microscopic anisotropy, and their diffusion-time dependence.

biophysics↗

bioRxiv2025

Formation of DNA duplexes in the presence of urea as a chaotropic agent.

Hybridization of fluorescent molecular probes, such as molecular beacons or linear molecular probes, with their molecular targets can be confirmed through fluorescence spectra. In this study, we investigate the interaction between fluorescent probes, specifically linear molecular probes, and their targets in the presence of chaotropic agents. Our findings show that double-stranded structures containing mismatched nucleotides (e.g., single-nucleotide polymorphisms) occupy lower energy levels (red shifted) compared to those without mismatched nucleotides. Molecular duplexes formed in buffers without chaotropic agents do not exhibit significant differences, independently on whether they contain mismatched nucleotides or are formed with perfectly matching targets. This effect appears in the presence of a naturally occurring chaotropic agent, urea, and was confirmed in the concentration range of 1 mM to 4 mM. These findings suggest that urea and similar agents may play a significant role in the formation of mismatched nucleotide structures.

molecular biology↗

bioRxiv2024

Differential cell type-specific function of the aryl hydrocarbon receptor and its repressor in diet-induced obesity and fibrosis

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor regulating xenobiotic responses as well as physiological metabolism. Dietary AhR ligands activate the AhR signaling axis in the intestine and throughout the organism, whereas AhR activation is negatively regulated by the AhR repressor (AhRR). While AhR-deficient mice are known to be resistant to diet-induced obesity (DIO), we here demonstrate that AhRR deficiency also leads to a robust, but not as profound protection from DIO and hepatosteatosis. Under conditions of DIO, AhRR-/- mice did not accumulate TCA cycle intermediates in the circulation in contrast to wild-type (WT) mice, indicating protection from metabolic dysfunction. This effect could be mimicked by dietary supplementation of AhR ligands in WT mice. Because of the predominant expression of the AhRR in myeloid cells, AhRR-deficient macrophages were analyzed for changes in metabolism and showed major metabolic alterations regarding oxidative phosphorylation and mitochondrial activity as well as increased expression of genes involved in de novo lipogenesis and mitochondrial biogenesis. Mice with a genetic deficiency of the AhRR in myeloid cells did not show alterations in weight gain after high fat diet (HFD) but demonstrated ameliorated liver damage compared to control mice. Further, deficiency of the AhR in myeloid cells also did not affect weight gain but led to enhanced liver damage and adipose tissue fibrosis compared to controls. Although conditional ablation of either the AhR or AhRR in myeloid cells did not recapitulate the phenotype of the global knockout, our findings suggest that enhanced AhR signaling in myeloid cells deficient for AhRR protects from diet-induced liver damage and fibrosis, whereas myeloid cell-specific AhR deficiency is detrimental.

immunology↗

bioRxiv2023

LOX-1 and MMP-9 inhibition attenuates the detrimental effects of delayed rt-PA therapy and improves outcomes after acute ischemic stroke

BackgroundAcute ischemic stroke triggers endothelial activation that disrupts vascular integrity and increases hemorrhagic transformation leading to worsened stroke outcomes. Recombinant-tissue plasminogen activator (rt-PA) is an effective treatment; however, its use is limited due to a restricted time window and high risk for hemorrhagic transformation, which in part may involve activation of metalloproteinases (MMPs) mediated through lectin-like oxidized LDL receptor 1 (LOX-1). This studys overall aim was to evaluate the therapeutic potential of novel MMP-9 and LOX-1 inhibitors in combination with rt-PA to improve stroke outcomes. MethodsThromboembolic rat stroke model was utilized to investigate the impact of rt-PA delivered 4h post-stroke onset as well as selective LOX-1 (BI-0115) and/or MMP-9 (JNJ0966) inhibitors given prior to rt-PA administration. Infarct size, perfusion, and hemorrhagic transformation were evaluated by MRI. Neurological function was assessed using sensorimotor functioning testing. Using an in vitro, human brain microvascular endothelial cell (HBMEC) model, cells were exposed to hypoxia plus glucose deprivation (3h)/reperfusion (12h) (HGD/R) and treated with rt-PA {+/-} an MMP-9 and LOX-1 inhibition cocktail. MMP-9 activity was determined with zymography, and endothelial barrier marker gene expression and LOX-1 levels were evaluated via qRT-PCR and western blot respectively. ResultsRt-PA treatment increased edema, hemorrhage, and worsened neurological outcomes post stroke. LOX-1 inhibition significantly improved neurological function and reduced edema after delayed rt-PA treatment. Hemorrhagic transformation, edema, and increased MMP-9 activity were attenuated by the MMP-9 inhibitor. Stroke induced increases in cerebrovascular LOX-1 expression correlated with increased MMP-9 activity and elevated activity correlated with increased edema, infarct volume, and decreased neurological function. In cultured HBMECs, LOX-1/MMP-9 inhibition differentially attenuated rt-PA-mediated increases in endothelial derived MMP-9 levels and activity, inflammation, and activation following HGD/R. ConclusionHere, we conclude that MMP-9/LOX-1 inhibition attenuates negative aspects of delayed rt-PA therapy leading to improved neurological function.

neuroscience↗

bioRxiv2023

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs

The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species this can affect the health of humans as well as livestock. Here we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realised.

evolutionary biology↗

bioRxiv2021

Mutation rate dynamics reflect ecological changes in an emerging zoonotic pathogen

While mutation is often deleterious, it can also be adaptive. Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study we investigate two factors that are predicted to influence the trade-off between the costs and benefits of mutation: ecology and genome size. To investigate the relationship between these factors and mutation rate we conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact ecology can have on the adaptive potential of bacterial pathogens.

evolutionary biology↗

bioRxiv2020

Capsular polysaccharide switching in Streptococcus suis modulates host cell interactions and virulence

Streptococcus suis serotype 2 strains can cause severe infections in both swine and humans. The capsular polysaccharide (CPS) of S. suis defines various serotypes based on its composition and structure. Though serotype switching from serotype 2 has been suggested to occur between S. suis strains, its impact on pathogenicity and virulence remains unknown. Herein, we experimentally generated S. suis serotype-switched mutants from a serotype 2 strain (SS2) that express the serotype 3, 4, 7, 8, 9, or 14 CPS (SS2to3, SS2to4, SS2to7, SS2to8, SS2to9, and SS2to14, respectively). The effects of serotype switching were then investigated with regards to classical properties conferred by presence of the serotype 2 CPS, including adhesion to/invasion of porcine tracheal epithelial cells, resistance to phagocytosis by murine macrophages, killing by murine and porcine whole blood, and dendritic cell-derived pro-inflammatory mediator production. Results demonstrated that these properties on host cell interactions were differentially modulated depending on the switched serotypes. Using a mouse model of systemic infection, SS2to8 was demonstrated to be hyper-virulent, with animals rapidly succumbing to septic shock, whereas SS2to3 and SS2to4 were less virulent than SS2 because of a reduced systemic inflammatory host response. By contrast, switching to serotype 7, 9, or 14 CPSs had little to no effect. Finally, development of clinical signs in a porcine model of infection was only observed following infection with SS2, SS2to7, and SS2to8. Taken together, these findings suggest that serotype switching can differentially modulate S. suis host cell interactions and virulence depending on the CPS type expressed. ImportanceStreptococcus suis serotype 2 is the most frequently type associated with swine and zoonotic infections. While the serotype 2 CPS is required for virulence and pathogenesis, little information is available regarding that of other serotypes and how differences in serotype can directly affect host cell interactions and virulence. Herein, we constructed serotype-switched mutants from a serotype 2 strain and demonstrated that serotype switching can shift and modulate the S. suis host cell interactions and virulence in vivo. Among the serotype-switched mutants, the mutant expressing the serotype 8 CPS, whose composition and structure are identical to that of the human pathogen Streptococcus pneumoniae serotype 19F, was hyper-virulent, whereas mutants expressing the serotype 3 or 4 CPSs had reduced virulence. These results demonstrate that serotype switching can drastically alter S. suis phenotype. Consequently, further importance and attention should be given to the phenomenon of serotype switching and the possible emergence of hyper-virulent isolates.

microbiology↗

bioRxiv2020

Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence

Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, a zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). While genome reduction is most often associated with bacterial endosymbionts, other correlates of symbiosis (reduced metabolic capacity, GC content, and the expansion of non-coding elements) are not found consistently in pathogens, and genome reduction in pathogens cannot be attributed to changes in intracellularity or host restriction. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria, and that the causes and consequences of genome reduction in pathogens are sometimes distinct from those in endosymbionts.

evolutionary biology↗

bioRxiv2020

Linking phenotype, genotype and ecology: antimicrobial resistance in the zoonotic pathogen Streptococcus suis

Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. Pigs receive more antimicrobials than most other livestock, and are a known source of zoonotic disease. We studied AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into "resistant" and "susceptible", highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multi-drug resistant isolates. And similar levels of resistance were found in pigs and humans from zoonotic regions. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many variants of small effect, appearing in a characteristic order. Our results confirm the potential for genomic data to aid in the fight against AMR, but also demonstrate that it cannot be tackled one species or one drug at a time.

microbiology↗