Biology subjects

Freund, M.

Publications and source records attributed to Freund, M..

12 recordsLinked to original sources

bioRxiv2026

Brain anatomy in major hormonal transition phases: Longitudinal and cross-sectional volume associations with menarche and menopause

BackgroundHormonal transition phases represent windows of increased neuroplasticity across the female lifespan. In this study, we aim to investigate the brain anatomical architecture of hormonal transition phases by directly comparing menarche, as a period of rising levels of steroid hormones, and menopause, as a time of declining levels. MethodsWe fit linear models on cross-sectional and linear mixed-effect models on longitudinal magnetic resonance imaging (MRI) datasets, to explore the effects of menarche onset (ABCD study data, Ncross-sectional=1274, Nlongitudinal=611) and transition into menopause (UK Biobank data, Ncross-sectional=1614, Nlongitudinal=212) on 66 cortical and 135 subcortical brain volumes, and to identify brain structures with opposing but regional overlapping effects in both periods. Models were adjusted for age and corrected for multiple comparison (P <.05; FDR-corrected). ResultsCross-sectionally, using a between-subject design, 83 brain volumes showed effects of menarche-onset and 17 volumes showed effects of menopause-transition. Of these, seven brain volumes were significantly affected by both transitional periods, showing opposing directional volume changes. Longitudinally, using a within-subject design, 56 brain volumes exhibited menarche effects, of which 46 replicated cross-sectionally. No menopause effect survived correction for multiple comparison, likely due to limited longitudinal sample size. ConclusionOur findings confirm regionally overlapping brain structural alteration between the two hormonal phases - menarche and menopause - showing the hypothesized opposite effect directions. Additionally, our results show the robustness of menarche effects, which converged across cross-sectional and longitudinal study designs. Taken together, our results contribute to a better understanding of hormone related neuroplasticity, emphasizing the importance of not only understanding individual phases, but understanding the overarching patterns across the female reproductive lifespan.

neuroscience↗

bioRxiv2025

Genome evolution and convergent innovation in the carnivorous plant Sarracenia purpurea

The repeated evolution of certain complex traits raises a fundamental question of how genomes generate ecological novelty while preserving developmental stability. Carnivorous pitcher plants, which modify a core organ of plant performance, the leaf, exemplify this challenge, yet the genomic basis of their convergent evolution has not been resolved. We present a chromosome-scale genome assembly for Sarracenia purpurea and analyze it alongside eight additional angiosperms spanning its parent clade Ericales and several other carnivorous lineages. The genome reveals extensive syntenic duplicate blocks arising from ancient polyploidy events, with diffuse, alternating dominant and recessive segments interleaved along chromosomes. Dominant regions are biased toward retained copies of dosage-sensitive regulatory genes, including AGO1, BRX, GATA11, ETC1 and RCD1. These genes highlight a conserved regulatory scaffold associated with leaf morphogenesis, including epidermal differentiation, auxin-mediated patterning, and redox-integrated coordination. By contrast, tandem gene duplications preferentially accumulate in structurally labile genomic regions and constitute a complementary, rapidly evolving component of the genome, enriched for ecological effector functions, including detoxification, glutathione-mediated redox buffering, antifungal pathways, and cuticle modification activities. Comparative union-based functional analyses across four carnivorous taxa reveal convergent recruitment of oxidative, transport, microbial-interaction, and cell-wall processes during independent trap evolution. Transcriptomic data confirm consistent activation of these pathways in pitchers. These findings demonstrate that complex traits arise through a genome-wide partitioning between polyploidy-derived, conserved developmental regulation and tandem-driven ecological specialization, here partitioning leaf architectural control from rapidly evolving functions associated with pitfall-based prey capture.

genomics↗

bioRxiv2025

Ca2+ signature-dependent control of auxin sensitivity in Arabidopsis

Plants must continually balance growth with arrest, especially under stress. Auxin signaling acts as a central regulatory hub in this process, yet the mechanisms that dynamically tune early auxin signalling in real time remain unknown. Here, we used the light-gated, Ca2+-permeable Channelrhodopsin 2 variant XXM2.0 to optogenetically impose defined Ca2+ signatures on Arabidopsis root cells. Repetitive light activation triggered cytosolic Ca2+ signals that in turn suppressed auxin-induced membrane depolarization and Ca2+ transients. Moreover, prolonged optogenetic Ca2+ stimulation affects auxin-responsive transcriptional reprogramming. As phenotypic output, reversible inhibition of root growth by suppressing cell division and elongation was observed. We further identify a candidate CaM7-CNGC14 module that likely mediates Ca2+-dependent gating of early auxin signalling. Our study thus introduces a synthetic biology approach to decompose calcium-auxin crosstalk in plant cells, and demonstrates that optogenetically imposed cytosolic Ca2+ signals act as dynamic regulators of auxin susceptibility in roots.

plant biology↗

bioRxiv2025

Impaired trap closure in the counting-deficient Venus flytrap mutant DYSCALCULIA is caused by cell wall biomechanics

Living in nutrient-poor environments, the carnivorous Venus flytrap Dionaea muscipula captures animal prey to compensate for this deficiency. Stimulation of trigger hairs located on the inner trap surface elicits an action potential (AP). While two consecutive APs result in fast trap closure in wildtype (WT) plants, sustained AP generation by the insect struggling to escape the trap leads to jasmonic acid (JA) biosynthesis, formation of the digestive "stomach", and release of enzymes needed to decompose the victim. The Dionaea muscipula DYSCALCULIA (DYSC) mutant is able to fire touch-induced APs, but unlike WT plants, it does not snap-close its traps after two consecutive APs. Moreover, DYSC plants fail to properly initiate the JA pathway in response to mechanostimulation and even wounding, a well-known JA-dependent process conserved among plants. As demonstrated in previous studies, this DYSC mutant defect is associated with impaired decoding of mechanostimulation (i.e. touch) -induced Ca2+ signals. External JA application to the trap, however, restores slow trap closure and digestive gland function in DYSC, while rapid trap closure is JA-independent and cannot be rescued by exogenous JA application. Higher frequency mechanostimulation and thus more APs, however, revealed that DYSC is still able to close its traps, albeit much slower than WT plants. To reveal the molecular underpinnings of DYSCs delayed trap movement, we generated a chromosome-scale Dionaea genome assembly and profiled gene expression. The refined transcriptomic analysis uncovered widespread misregulation of cell wall-related genes in DYSC, implicating altered cell wall plasticity in the sluggish mutant. Cell indentation studies by atomic force microscopy revealed a strictly localized and strikingly enhanced stiffening of the cell wall for DYSC that may hinder rapid trap closure and snap buckling. Together, these genomic, transcriptomic, and biophysical data identify cell wall elasticity as a key constraint on voltage and Ca2+ dependent trap kinetics. This finding documents the interrelationship between mechanosensing and Ca2+ signaling in the ultrafast capture organ of the Venus flytrap.

plant biology↗

bioRxiv2025

Convergent losses of arbuscular mycorrhizal symbiosis in carnivorous plants

Across evolutionary scales, lineages acquire and lose traits and associated genes. Most land plants form arbuscular mycorrhizal (AM) symbiosis, an ancient trait for enhanced nutrition that was convergently lost in some clades. Carnivory, another nutritional trait, is a more recent adaptation that has convergently arisen in several angiosperm orders. The two biotic interactions similarly help plants acquire mineral nutrients, raising the question of whether they can coexist. However, the mycorrhizal status of carnivorous plants has long remained speculative. Here, we surveyed the occurrence of AM-associated genes in five angiosperm orders harbouring carnivorous species, revealing convergent losses of the AM trait either coincident with or predating the emergence of carnivory. Exceptionally, the carnivorous plant species Roridula gorgonias retains symbiosis-related genes and forms arbuscules upon inoculation assays, demonstrating the two nutritional strategies, although rare, can coexist. The youngest carnivorous lineage, Brocchinia reducta, showed signatures of the early stages of AM trait loss, as reflected by its gene retention and AM colonization patterns. An AM-associated CHITINASE gene encodes a digestive enzyme in the Australian pitcher plant Cephalotus, suggesting gene co-option. These findings illuminate the largely unexplored processes by which plant nutritional strategies evolve and supplant one another over time.

plant biology↗

bioRxiv2024

Molecular mechanism of thyroxine transport by monocarboxylate transporters

Thyroid hormones (the common name for prohormone thyroxine and the bioactive form triiodothyronine) control major developmental and metabolic processes. Release of thyroid hormones from the thyroid gland into the bloodstream and their transport into target cells is facilitated by plasma membrane transporters, of which monocarboxylate transporter (MCT)8 and the highly homologous MCT10 are most important. Patients with MCT8 mutations suffer from a severe neurodevelopmental and metabolic disorder, however, the molecular mechanism underlying thyroid hormone transport is unknown. Using cryogenic-sample electron microscopy (cryo-EM), we determined the ligand-free and thyroxine-bound human MCT8 structures in the outward-open state and the thyroxine-bound human MCT10 in the inward-facing state. Our structural analysis revealed a network of conserved gate residues involved in conformational changes upon thyroxine binding, triggering ligand release on the opposite compartment. We then determined the structure of a folded, but inactive patient-derived MCT8 mutant, indicating a subtle conformational change which explains its reduced transport activity. In addition, we determined the structure of MCT8 bound to its inhibitor silychristin, revealing an interaction with residues essential to drive transition to the inward-facing state, thereby locking the protein in the outward-facing state. This study provides molecular and structural insights into normal and disordered thyroid hormone transport.

biochemistry↗

bioRxiv2023

Assessing adverse effects and unspecific effects of transcutaneous spinal direct current stimulation (tsDCS)

BackgroundTranscutaneous spinal direct current stimulation (tsDCS) is a relatively recent method for non-invasively modulating neuronal activity in the human spinal cord. Despite its growing prominence, comprehensive studies addressing its potential adverse effects (AEs) and unspecific effects (UEs) are lacking. ObjectiveIn this study, we conducted a systematic investigation into the potential AEs and UEs of tsDCS in healthy volunteers. MethodsWe used a randomized double-blind within-participant design, employing anodal, cathodal and sham tsDCS of the thoracolumbar spinal cord. Our approach involved a newly-developed structured questionnaire (to assess subjectively-reported AEs) in combination with tsDCS-concurrent recording of skin conductance, cardiac and respiratory activity (to assess UEs in bodily state). ResultsThe most frequently participant-reported AEs were sensations of burning, tingling, and itching, although they were largely described as mild; skin redness (experimenter-reported) occurred even more frequently. Importantly, when comparing AEs between active and sham tsDCS via frequentist and Bayesian analysis approaches, the results were largely in favour of no difference between conditions (with the exception of skin redness). A similar picture emerged for most UE metrics, suggesting that tsDCS does not induce changes in bodily state, at least as measured by our autonomic nervous system metrics. ConclusionWe believe that the strategy employed here could serve as a starting point for a systematic AE and UE assessment in clinical populations, longitudinal designs and when stimulating different spinal sites. Taken together, our results contribute to assessing the tolerability, safety and specificity of tsDCS, in order to further the investigation of spinal cord function in health and disease.

neuroscience↗

bioRxiv2023

Increasing equity in science requires better ethics training: a course by trainees, for trainees

Despite the profound impacts of scientific research, few scientists have received the necessary training to productively discuss the ethical and societal implications of their work. To address this critical gap, we - a group of predominantly human genetics trainees - developed a course on genetics, ethics, and society. We intend for this course to serve as a template for other institutions and scientific disciplines. Our curriculum positions human genetics within its historical and societal context and encourages students to evaluate how societal norms and structures impact the conduct of scientific research. We demonstrate the utility of this course via surveys of enrolled students and provide resources and strategies for others hoping to teach a similar course. We conclude by arguing that if we are to work towards rectifying the inequities and injustices produced by our field, we must first learn to view our own research as impacting and being impacted by society.

genetics↗

bioRxiv2023

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype with five complete sets of syntenic chromosomes (2n = 10x = 80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbor three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent because duplicates were enriched with Nepenthes-specific genes with tissue-specific expression, including those expressed in trapping pitchers. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes experiencing relaxed purifying selection to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.

plant biology↗

bioRxiv2021

Interleukin-11 plays a key role in human and mouse alcohol-related liver disease

BackgroundAlcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide with limited treatment options. Interleukin-11 (IL-11) is a pro-fibrotic, pro-inflammatory cytokine with increasingly recognized toxicities in parenchymal and epithelial cells. AimThe aim of this study was to explore the prognostic value of IL-11 serum levels in patients suffering from AH and cirrhosis of various etiology and to understand the role of IL-11 in experimental ALD. MethodsIL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort including 186 patients. Ethanol-fed wildtype mice were treated with a neutralizing murine IL-11 receptor-antibody (anit-IL11RA) and thereafter examined for severity signs and markers of ALD. ResultsHuman IL-11 serum concentration and liver tissue expression increased with severity of liver disease and were most pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 picograms/milliliter was a MELD independent risk factor for transplant-free liver disease survival in patients with compensated and decompensated cirrhosis. Findings were confirmed in an independent cohort. In mice, severity of alcohol-induced liver inflammation was positively correlated to enhanced hepatic IL-11 expression. Pretreatment with a neutralizing anti-IL11RA inhibited hepatic inflammation and mice were protected from ethanol-induced liver injury. In comparison to IgG-control, ethanol-fed mice treated with anti-IL11RA showed decreased steatosis, hepatic neutrophil infiltration, and expression of pro-inflammatory cytokines. ConclusionIL-11 plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signaling might be a therapeutic option in human ALD, particularly AH.

immunology↗

bioRxiv2017

Probabilistic fine-mapping of transcriptome-wide association studies

Transcriptome-wide association studies (TWAS) using predicted expression have identified thousands of genes whose locally-regulated expression is associated to complex traits and diseases. In this work, we show that linkage disequilibrium (LD) among SNPs induce significant gene-trait associations at non-causal genes as a function of the overlap between eQTL weights used in expression prediction. We introduce a probabilistic framework that models the induced correlation among TWAS signals to assign a probability for every gene in the risk region to explain the observed association signal while controlling for pleiotropic SNP effects and unmeasured causal expression. Importantly, our approach remains accurate when expression data for causal genes are not available in the causal tissue by leveraging expression prediction from other tissues. Our approach yields credible-sets of genes containing the causal gene at a nominal confidence level (e.g., 90%) that can be used to prioritize and select genes for functional assays. We illustrate our approach using an integrative analysis of lipids traits where our approach prioritizes genes with strong evidence for causality.

genetics↗

bioRxiv2017

Leveraging polygenic functional enrichment to improve GWAS power

Functional genomics data has the potential to increase GWAS power by identifying SNPs that have a higher prior probability of association. Here, we introduce a method that leverages polygenic functional enrichment to incorporate coding, conserved, regulatory and LD-related genomic annotations into association analyses. We show via simulations with real genotypes that the method, Functionally Informed Novel Discovery Of Risk loci (FINDOR), correctly controls the false-positive rate at null loci and attains a 9-38% increase in the number of independent associations detected at causal loci, depending on trait polygenicity and sample size. We applied FINDOR to 27 independent complex traits and diseases from the interim UK Biobank release (average N=130K). Averaged across traits, we attained a 13% increase in genome-wide significant loci detected (including a 20% increase for disease traits) compared to un-weighted raw p-values that do not use functional data. We replicated the novel loci in independent UK Biobank and non-UK Biobank data, yielding a highly statistically significant replication slope (0.66-0.69) in each case. Finally, we applied FINDOR to the full UK Biobank release (average N=416K), attaining smaller relative improvements (consistent with simulations) but larger absolute improvements, detecting an additional 583 GWAS loci. In conclusion, leveraging functional enrichment using our method robustly increases GWAS power.

genetics↗