Biology subjects

Mueller, M.

Publications and source records attributed to Mueller, M..

At least 19 recordsLinked to original sources

bioRxiv2026

How goals shape naturalistic memories: bias in gaze and narrative recall

Episodic memories are thought to represent information framed by our individual perception and goals, yet personal experiences are hard to evaluate externally. Due to novel methodological advances, we could now trace the development of such goal-shaped memories in a naturalistic experimental setting. We recorded eye-tracking while participants encoded episodic-like memories, and later recorded participants freely narrating their experiences. Naturalistic goal-states were induced by introducing a secret job, which promised to reward participants later for person-based or space-based information. Using computer-vision based semantic segmentation of visual scanning behaviour in movie scenes and data-driven coding of free recall performance, we show that these goals increasingly shift attention during memory encoding and systematically bias narration during retrieval to goal-relevant dimensions. Our findings highlight that we can use data-driven methodology to observe how naturally occurring or induced biases shape how we perceive and remember the world.

neuroscience↗

bioRxiv2026

GPNMB enables lysosomal adaptation required for myelin clearance and nerve regeneration after peripheral nerve injury

Recovery from peripheral nerve injury involves coordinated axonal and immune repair programs that promote tissue regeneration. However, the mechanisms regulating immune-mediated repair remain incompletely understood. Here, we demonstrate that glycoprotein non-metastatic melanoma protein B (GPNMB) is a key regulator of repair processes following peripheral nerve injury. In a mouse sciatic nerve crush model, loss of Gpnmb impaired functional recovery after injury. MRI and histological analyses revealed persistent myelin debris accumulation, defective debris clearance, and impaired macrophage lysosomal function within injured nerves. Mechanistic studies showed that GPNMB-deficient human iPSC-derived macrophages exhibited impaired lysosomal adaptation, reduced lysosomal fitness, and defective processing of myelin-associated cargo, resulting in inefficient degradation of injury-associated material. These defects were accompanied by impaired acquisition of repair-associated cellular programs. Together, our findings identify GPNMB as a critical regulator of lysosome-dependent repair programs during nerve regeneration and demonstrate that efficient GPNMB-dependent myelin processing is required for functional recovery following peripheral nerve injury.

neuroscience↗

bioRxiv2026

Effector-host networks in the barley powdery mildew pathosystem reveal significant targeting of ubiquitin-associated proteins and transcriptional regulators

- The ascomycete fungal pathogen Blumeria hordei (Bh) is predicted to secrete over 530 effector proteins to infect barley and cause powdery mildew disease, yet their individual and collective functions are largely unexplored. We used yeast two-hybrid next-generation interaction screening (Y2H-NGIS) to probe the host targets of 48 Bh candidate secreted effectors (CSEPs), including multiple AVRA effectors that are recognized by MLA nucleotide-binding leucine-rich repeat (NLR) receptors. - Y2H-NGIS and subsequent binary retesting identified 356 high-confidence protein-protein interactions (PPI) among Bh CSEPs, MLA NLR fragments, and barley proteins. We uncovered unique and shared host targets, including numerous proteins involved in ubiquitin-associated processes, gene expression, immune and kinase signaling, metabolism, and vesicle trafficking. - We identified a host protein (HvCAP2) that interacts with MLA and at least five Bh effectors, as well as additional effector-host PPI that correlate with loss of recognition of AVRA13 and AVRA6 by MLA13 and MLA6, respectively. - Results were integrated with an interolog-based barley interactome (HvInt) to assemble a host-pathogen network of 1248 proteins and 1701 interactions. This PPI resource can serve as a platform for functional investigations into the molecular basis of powdery mildew pathogenesis and host recognition.

plant biology↗

bioRxiv2026

A Normative Model Reveals Functional Optimization of Synaptic Nano-Architecture

Super-resolution microscopy approaches have revealed that synaptic proteins are not randomly distributed within individual synapses. Rather, they form sub-synaptic clusters that may be coordinated between the synaptic compartments, thereby forming transsynaptic nanocolumns. However, the functional significance of this nano-architecture remains under debate. In particular, it is unclear whether the positions of synaptic proteins optimize a specific cost function. Here, we present a normative modeling framework that integrates synaptic nano-architecture imaged with STED and dSTORM microscopy with synaptic transmission recorded with electrophysiology at the Drosophila neuromuscular junction (NMJ). Model-based quantification showed that clusters of Unc13A, which likely demark presynaptic release sites, and postsynaptic glutamate receptors (GluRs) adopt aligned ring-like arrangements in individual synapses. We developed an analytical description of GluR activation relative to presynaptic release position, enabling to link super-resolution imaging data with recorded postsynaptic current amplitudes without relying on costly Markov chain Monte Carlo (MCMC) simulations. Our model predicts that glutamate released from a single vesicle spreads across the entire receptor population. Given this spread, the postsynaptic current amplitude is maximized when glutamate is released close to the active zone (AZ) center, in contradiction to the observed offset of Unc13A clusters. However, the observed relative positions of Unc13A and GluR clusters maximize the postsynaptic current amplitude and minimize the delay between vesicle release and receptor activation during multivesicular release. Hence, transsynaptically-aligned Unc13A-GluR rings optimize for multivesicular but not univesicular release. Given that multivesicular release is mainly observed during enhanced presynaptic release at the Drosophila NMJ, transsynaptic nano-architecture may be adapted to elevated presynaptic release states.

neuroscience↗

bioRxiv2026

PAIP1 couples mRNA export to cytoplasmic mRNP remodeling and poly(A) homeostasis

Messenger ribonucleoproteins (mRNPs) acquire distinct protein compositions as they move from the nucleus to the cytoplasm, yet how this transition is coordinated and how inefficient remodeling affects downstream mRNA metabolism remains poorly understood. Here, we identify PAIP1 as a metazoan cofactor of the mRNA export ATPase DDX19. By binding a conserved N-terminal motif in DDX19, PAIP1 is recruited to the nuclear pore, where it promotes exchange of the nuclear poly(A)-binding protein PABPN1 for cytoplasmic PABPC1, thereby coupling mRNA export to cytoplasmic mRNP maturation. PAIP1 depletion alters cytoplasmic mRNP composition, mRNA stability and poly(A)-tail homeostasis. In Drosophila embryos, where poly(A)-tail regulation of maternal mRNAs directs early development, maternal PAIP1 depletion shortens poly(A)-tails, delays zygotic genome activation, and causes severe developmental defects. Our findings identify an export-coupled mRNP maturation pathway linking PABP exchange to downstream mRNA metabolism.

molecular biology↗

bioRxiv2026

Selective covalent-allosteric tools to dissect Akt2

The protein kinase Akt and its isoforms play a crucial role in various diseases. Unique functions of the individual isoforms (Akt1, Akt2, Akt3) might be essential for survival in malignancies. Particularly for Akt2, it was reported that a knock-out led to diabetic phenotype and might be correlated with clinically adverse hyperglycemic effects observed in pan Akt-treatment. Enduring failure of Akt inhibitors in the clinic indicates the necessity for a thorough understanding of the underlying biology, preferably by using highly isoform-selective small molecules. Here we report the structure-guided development of Akt2-selective covalent-allosteric probe molecules, that can be successfully modified within a complex environment using biorthogonal chemistry. Thus, enabling first Akt2-specific pull-down studies and the use in functional studies, such as selective fluorescent labeling in cellular systems. These chemical probes expand our toolbox to dissect the critical questions of Akt2s function in health and disease, thereby paving the way for novel therapeutic strategies based on thorough mechanistic insights.

Cancer Biology↗

bioRxiv2026

Sexually dimorphic effects of mutations in ccRCC driver genes in renal proximal tubule cells

Clear cell renal cell carcinoma (ccRCC) arises more frequently in men than in women, but it remains unclear why this is the case. Mouse models that mimic the truncal mutation of the two most commonly affected tumor suppressor genes in human ccRCC revealed that the transcriptional effects of Vhl or Vhl/Pbrm1 mutation in male and female proximal tubule cells only partially overlap. Cellular responses to mutations in these genes were also sex-specific. Vhl and Vhl/Pbrm1 mutation in females, but only Vhl/Pbrm1 mutation in males, induced the accumulation of PLIN2-coated lipid droplets. The accumulation of optically-clear lipid droplets, reflecting the hallmark clear-cell histological feature of ccRCC, only arose in Vhl/Pbrm1 mutant male mice. Consistent with lipotoxic tubular damage, markers of tubular repair and ongoing epithelial cell proliferation correlated with the lipid accumulation phenotypes. Vhl/Pbrm1 mutation caused stronger clonal expansion than Vhl mutation in males, but not in females. These findings suggest that there are likely to be sexual dimorphisms at the very earliest stages of ccRCC evolution that result from the interplay of intrinsic and mutation-induced transcriptional differences between male and female proximal tubule cells.

cancer biology↗

bioRxiv2026

S-Adenosyl-D-methionine as a Non-Physiological Substrate for a Wide Range of SAM-Dependent Enzymes

The ability of SAM-dependent enzymes to accept S-adenosyl-D-methionine [D-SAM, (SS,RC)-SAM] instead of the native cofactor S-adenosyl-L-methionine [L-SAM, (SS,SC)-SAM] remains largely unexplored. Challenging the stereochemical preference of SAM-dependent enzymes, we investigated the ability of different enzyme classes to accept D-SAM. Contrary to common assumptions, the tested N- and O-methyl transferases (MTs), as well as one of the examined C-MTs accepted D-SAM. Docking studies suggest that acceptance of D-SAM by C-MTs may be influenced by the angle between the transferable methyl group of SAM and the nucleophilic carbon of the substrate, along with enzyme and substrate flexibility. In addition to conventional MTs, the radical SAM glutamine C-MT QCMT showed low but detectable methylation activity with D-SAM. Furthermore, the azetidine-2-carboxylic acid synthase AzeJ not only uses D-SAM but also incorporates the stereocentre of D-methionine into the cyclic amino acid product. The pyridoxal 5'-phosphate (PLP)-dependent enzyme 1-aminocyclopropyl-1-carboxylic acid synthase (ACCS) also showed detectable turnover with D-SAM. These findings broaden the understanding of enzyme stereoselectivity, provide an overview of D-SAM-utilising enzymes, and identify first enzyme systems that may serve as starting points for engineering efforts aimed at shifting cofactor preference towards D-SAM.

biochemistry↗

bioRxiv2026

Genomic Prediction Enables Provenance-Aware Selection in 1 Sessile Oak (Quercus petraea) using Foliar Physiological Traits

Climate change is reshaping the adaptive landscape of forest ecosystems, demanding more efficient strategies to identify and deploy resilient tree genotypes. Genomic prediction offers a powerful framework to accelerate selection for complex physiological traits underlying climate adaptability in long-lived species such as sessile oak (Quercus petraea (Matt.) Liebl.). Here, we conducted genomic prediction for three key physiological traits carbon isotope composition, nitrogen isotope composition, and the carbon-to-nitrogen content ratio (C/N ratio) measured in 746 trees genotyped with dense genome-wide markers ([~]580,000 SNPs). High genomic heritabilities were estimated across traits, with within-year prediction accuracies (Pearsons r between genomic estimated values and observed phenotypes) reaching 0.77. Notably, across-year and across-provenance predictions remained substantial (0.41 < r < 0.82), with predictability declining with increasing genetic distance (FST) between training and test provenances for nitrogen isotope composition and C/N ratio. In addition, GWAS-guided SNP preselection increased heritability capture by [~]15% relative to random SNP subsets. And, the pronounced provenance-by-environment interactions observed indicated substantial phenotypic plasticity in these traits. These results demonstrate the strong potential of applying genomic prediction to foliar physiological traits as polygenic predictors for climate adaptation in plants, support provenance-aware breeding to improve forest establishment, and provide practical strategies for deploying genomic prediction in long-lived species.

genetics↗

bioRxiv2026

Metabolic specialization structures gut bacterial niches and drives colorectal cancer progression

Despite the established association between the gut microbiome and colorectal cancer (CRC), the functional distinction between microbial passengers and drivers of CRC progression remains unresolved. Here, we collected stool, blood, as well as paired tumor, and normal mucosa tissues from seventy-seven CRC patients to characterize the systemic and localized impact of the gut microbiome on early- and late-stage CRC. By deep shotgun metagenomic sequencing, we identified distinct bacterial species and functions residing in tumor versus normal mucosa, highlighting an enrichment of oral-associated bacteria in tumor tissues. Several of these species remained undetected in the stool microbiome analysis. We further combined bacterial culturing with untargeted metabolomics of bacteria enriched in tumor and normal mucosa tissues, revealing distinct clusters of metabolic potential. Functional testing of multiple members from one cluster comprising both tumor- and mucosa-enriched species revealed Leptotrichia wadei as a pro-tumorigenic bacterium in a murine CRC model. Single-nucleus RNA sequencing and in vitro experiments further demonstrated that L. wadei and its secretome induces M2 macrophage polarization to promote tumor growth. Overall, our study shows that metabolic specialization structures microbial colonization niches, while species-specific metabolic outputs identify functional drivers of CRC progression, and uncovers L. wadei as an oncogenic bacterium in CRC.

microbiology↗

bioRxiv2026

Enhanced 2D structured illumination microscopy: super-resolution with optical sectioning and reduced reconstruction artifacts

Structured Illumination Microscopy (SIM) provides imaging with spatial super-resolution, as well as optical sectioning capability, without relying on specialized fluorescent dyes. 2D and 3D variants of this method exist, but most bespoke implementations are 2D-SIM, because it is easier to realize and modify than 3D-SIM. 2D-SIM systems, however, often experience reconstruction artifacts from out-of-focus contributions, especially when pushing for high lateral spatial resolution in thicker samples. We present enhanced 2D-SIM, an approach to 2D-SIM where both, coarse patterns optimized for removing out-of-focus background, and fine patterns optimized for resolution improvement beyond the diffraction limit are used. In combination, this achieves 2D-SIM reconstructions with high contrast, spatial super-resolution, and significantly reduced reconstruction artifacts. We present the theoretical framework of this technique, and provide enhanced 2D-SIM imaging results of liver sinusoidal endothelial cells stained with fluorophores emitting at visible and near-infrared wavelengths. Quantitative comparisons of power spectral distribution and image resolution are demonstrated.

biophysics↗

bioRxiv2026

Expectation of aversive outcomes drives multimodal integration of behavioural, physiological and neural activations during human fear retrieval and generalisation

Classical fear conditioning describes how neutral cues acquire a threat value, yet how learned associations are retrieved and generalised across similar stimuli specifically is an ongoing debate. We combined behavioural ratings, physiological measures, and fMRI in a two-day classical fear conditioning paradigm to characterize acquisition, retrieval, and generalisation across modalities. Twenty-five healthy participants completed acquisition trials on Day 1 and retrieval and generalisation trials on Day 2 using conditioned (CS+, CS-) and graded generalisation stimuli (GS). Outcomes included trial-wise US expectancy ratings, pre/post fear and arousal ratings, skin conductance responses (SCR), pupil dilation, and ROI-based fMRI (amygdala, hippocampus, insula, periaqueductal gray (PAG), locus coeruleus). Acquisition yielded robust CS+/CS-discrimination in behavioural ratings and increased BOLD responses in bilateral insula and PAG. During retrieval, US-expectancy ratings indicated early retrieval of CS contingency. The fMRI results showed greater BOLD activity during CS+ presentations than during CS-presentations in bilateral hippocampus, left insula and right PAG. Additionally, hippocampus-insula coupling increased. Critically, parametric modulation during retrieval revealed that trial-wise mean US-expectancy modulated BOLD responses in left insula and right PAG, with a trend in left hippocampus. Across generalisation, US-expectancy and pupil dilation responses followed graded profiles, which could be explained by a Gaussian model, whereas SCR generalised, but was not captured by a Gaussian model. Parametric modulation by US-expectancy correlated with BOLD activity in left PAG, with a trend in right hippocampus. Stimulus identity explained variance in bilateral insula and left PAG. Findings converge on a hippocampus-insula-PAG network that retrieves learned predictions, and scales defensive output according to similarity-based threat probability, linking subjective, physiological, and neural outcomes.

neuroscience↗

bioRxiv2025

N, N-Dimethyltryptamine and harmine formulation shifts metastable topography sequences in the cortex

Classic serotonergic psychedelics are potent modulators of conscious awareness, yet the principles governing their effects on the temporal dynamics of brain activity remain unclear. Dominant theories propose that psychedelics increase the signal diversity and metastability of neural states, but whether this reflects a simple randomization of activity or a more structured reorganization is unknown. Here, we used high-density EEG (n=25) in a double-blind, placebo-controlled study to delineate the effects of an ayahuasca-inspired formulation (intranasal N,N-DMT and buccal harmine) on the syntax of whole-brain functional states. Using microstate analysis, we show that psychedelic states induced by DMT and harmine are characterized by a profound acceleration of neural dynamics, evidenced by a reduced microstate duration and an increased frequency of state transitions. Despite that, the sequence of microstates became less random, as indicated by a higher first-order Markov statistic. This syntactic restructuring involved a systematic de-prioritization of transitions into one state (M2) and a corresponding increase in the prevalence and accessibility of two other states (M3 and M5). These findings reveal that the psychedelic state leads to a syntactically reconfigured state of heightened metastability. By showing that psychedelics both lead to an accelerated exploration of an expanded repertoire of neural states governed by increased syntactic structure, our findings improve our understanding of neural metastability in psychedelic states.

neuroscience↗

bioRxiv2025

The PDE4D ortholog Dunce suppresses memory in Drosophila melanogaster

The regulation of cAMP concentration is a key component of the mechanisms underlying learning and memory. In Drosophila melanogaster, the cAMP-specific phosphodiesterase mutant dunce1 results in increased levels of cAMP but poorer associative short-term memory and anesthesia-resistant memory. This raises the question of how elevated cAMP levels can cause defects in both short-term and long-term memory. To answer this question, we analyzed associative olfactory learning and memory in Drosophila larvae of both sexes with the isoform-specific dunce{Delta}143 mutation. Flies with this mutation exhibited better learning than flies with the dunce1 mutant. The memory facilitated by dunce{Delta}143 was stable and easily reversable. The improvement in memory was also traced to a defined subset of neurons. A comparison of the subcellular localization of Dunce isoforms indicates that the regulation of cAMP in the soma suppresses early memory formation. We revealed that Dunce regulates at least two different aspects of learning and memory, specifically, preventing the premature formation of memory and facilitating the formation of memory after multiple training sessions. The different functions of Dunce might be due to different cell types. Significance StatementIn model systems such as Aplysia and mice, elevated cAMP levels are associated with increased learning and memory performance; in contrast, Drosophila dunce mutants with elevated cAMP levels exhibit memory decline. Here, we revisited the function of the phosphodiesterase 4D ortholog Dunce and showed that Dunce both promotes and inhibits memory formation.

neuroscience↗

bioRxiv2025

Network Adaptability Governs Resilience and Susceptibility to Social Defeat

Stress resilience is defined as the ability to maintain mental health after adversity. In humans, resilience is marked by threat-safety discrimination and extinction of fear, whereas susceptibility involves fear generalization and extinction resistance. Using a translational mouse model of chronic social defeat stress combined with preregistered multimodal brain imaging, we investigated structural and network-level markers of resilience, susceptibility, and threat learning. Resilience was characterized by preserved dentate gyrus integrity, greater microstructural complexity in prefrontal regions, and signatures consistent with enhanced inhibitory gating within amygdalar circuits. Susceptibility, in contrast, involved reduced dentate gyrus complexity and diminished microstructural flexibility, with a weaker but parallel pattern in the basolateral amygdala. Impaired threat learning was linked to compromised CA1/CA2 integrity and reduced pons connectivity, highlighting hippocampal-brainstem interactions in memory consolidation. Overall, these findings show that resilience emerges from adaptive network reorganization, whereas susceptibility and impaired learning reflect distinct dysfunctions, underscoring individual coping differences even among genetically identical animals.

neuroscience↗

bioRxiv2025

Resolving temporal threat uncertainty by observational learning involves the amygdala, hippocampus and anterior insula

By observing others experiences, humans learn about threats while avoiding firsthand dangers. Yet, previous neuroscience research has focused on observational threats that are predictable. In firsthand learning, temporally predictable and unpredictable threats can be mechanistically discerned. In this study, we developed a novel observational paradigm in which participants learned from predictable and unpredictable observational threats, as well as a no-threat condition. Participants encountered the same conditions during an expression phase to investigate how the brain encodes predictive and unpredictive threat cues observed in others. Participants in Experiment 1 (n = 20, 14 female, 6 male) and Experiment 2 (n = 23, 9 female, 1 non-binary, 13 male) successfully learned threat contingencies, showing heightened threat expectations for predictive cues and unpredictable condition-onsets. Behavioral findings converged with neural (fMRI, Experiment 2) responses in the anterior insula during the expression phase. Reflecting the dynamic process of learning, amygdala activation in response to predictive threat cues displayed a linear decrease across trials. Interestingly, BOLD responses to others pain that was predictable, were enhanced within the amygdala, insula and hippocampus, compared to unpredictable conditions. Our findings suggest that humans can learn to resolve temporal threat uncertainty, through the observation of others. The present work thereby contributes to understanding the social aspects of fear and anxiety disorders.

neuroscience↗

bioRxiv2025

Three pathways feed the folate-dependent one carbon pool for growth and virulence of Listeria monocytogenes

The bacterium Listeria monocytogenes can grow in the cytoplasm of infected human cells, but there it relies on specific biosynthetic pathways for intracellular nutrient supply. We previously found that the glycine cleavage system (GCS) is needed for intracellular growth. The GCS decarboxylates glycine for generation of 1C-tetrahydrofolates (1C-THF), folate-dependent one carbon donors needed for biosynthesis of other metabolites. We continued our studies on the GCS and show that a L. monocytogenes {Delta}gcvPAB mutant, lacking the GCS glycine dehydrogenase, is attenuated without resembling the phenotype of classical virulence factor mutants. The {Delta}gcvPAB mutant also grew poorly in synthetic medium, explained by the presence of glycine that was toxic for this strain. Selection of glycine resistant suppressors yielded a survivor, in which the N- and C-terminal parts of the formate-tetrahydrofolate ligase (fhs) gene, which is naturally separated into two parts by a premature stop codon in the L. monocytogenes reference strain EGD-e, were reassembled into a full-length open reading frame. Like the GCS, Fhs also feeds the 1C-THF pool and its restoration cured the virulence defects of the {Delta}gcvPAB mutant. Another suppressor had a mutated glyA gene, encoding serine hydroxymethyltransferase, and combinatorial deletions of gcvPAB and glyA in fhs- and fhs+ backgrounds demonstrated a role of GlyA in 1C-THF metabolism. Our results show that three pathways feed the 1C-THF pool to support growth and virulence of L. monocytogenes and represent the first example of the spontaneous reactivation of a L. monocytogenes gene that is inactivated by a premature stop codon.

microbiology↗

bioRxiv2025

Jlp2 is an RQC complex-independent release factor acting on aberrant peptidyl-tRNA, protecting cells against translation elongation stress

Ribosome stalling generates aberrant nascent peptides that remain tethered to the large ribosomal subunit following ribosome splitting. Such peptidyl tRNA:60S complexes are processed by the Ribosome associated Quality Control (RQC) pathway, where Ltn1 and Rqc1 mediate K48 linked ubiquitination and Rqc2 adds CAT tails to the nascent peptides.Subsequently, Vms1 releases the peptides from tRNA, enabling their proteasomal degradation. However, alternative mechanisms that process these stalled intermediates remain poorly defined. In this study, we identify Jlp2 as a novel factor involved in translation quality control. We find that Jlp2 is a release factor that catalyzes peptide release from tRNA and suppresses excessive CAT tailing when Ltn1-dependent ubiquitination is compromised. We define its ribosome binding properties, substrate scope, and critical residues required for peptide release. Our data support a model in which Jlp2-mediated peptide release constitutes an alternative quality control mechanism to safeguard cells during ribosome stalling and conditions of RQC failure or insufficiency.

molecular biology↗