Biology subjects

Müller, M. M.

Publications and source records attributed to Müller, M. M..

6 recordsLinked to original sources

bioRxiv2026

Domain Insertion Improves the Precision of a CRISPR Adenine Base Editor

Adenine base editors (ABEs) enable efficient A*T to G*C conversion, but their broad activity windows frequently cause unintended bystander edits. We hypothesized that insertion of a bulky, inert protein domain into the base editor would limit the effective reach of the deaminase, thereby preferentially directing editing to the intended target adenine. Here, we systematically map domain insertion sites within the high-activity TadA8e adenine base editor using structure-guided design and computational inference. We find that TadA8e accepts domain insertions at multiple surface sites, with overall activity and editing window width dependent on insert position rather than domain identity. Excitingly, inserting domains at residue L68 preserved robust editing across multiple genomic loci while tightly focusing the editing window around position 5. Insertion of superfolder GFP at this site produced a base editor variant with a narrower editing window, the ability to track edited cells by fluorescence, and markedly reduced Cas-independent off-target editing. Our work highlights domain insertion engineering as a powerful strategy to create more focused and precise CRISPR base editors.

synthetic biology↗

bioRxiv2025

Human performance in the Traveling Salesman Problem is influenced by spatial scale

Like many other animals, we humans frequently face complex route optimization problems when planning journeys between multiple locations. Several strategies can be employed to approach such Traveling Salesman Problems. However, these may be strongly constrained by spatial scales, for instance if the goal is to navigate in a supermarket, in a city, or across a continent. Here, we monitored the route optimization performances of human subjects collecting objects in a video game simulating 3D environments at various spatial scales. Unexpectedly, route optimization performances peaked at intermediate spatial scales, where participants could use global optimization strategies. At very large and very small spatial scales, however, participants predominantly employed less efficient local optimization strategies. At the very large scale, the considerable distances between objects prevented them from being seen all at once, making global planning difficult. At the very small scale, participants reported having chosen the shortest path, although they did not. This mismatch between perceived and actual performances suggests suboptimal alternatives were sufficiently short to be considered equivalent to the optimal route. Spatial scale thus strongly influences route planning in human navigators and may determine the spatial behaviors of a wide range of animals facing similar routing problems in their everyday lives.

animal behavior and cognition↗

bioRxiv2025

Uncovering persistent biases in human path integration by separating left and right trials

Navigation ability strongly varies between humans. Careful analysis of errors occurring in navigation, or indeed any cognitive process, offers insight into the underlying mechanisms at different levels. While analyses at the individual level allow nuanced identification of error persistences across conditions and time, the population level facilitates generalisation but precludes conclusions about lower-level phenomena. Regarding the critical navigation mechanism of path integration - the continuous tracking of navigated paths for self-localisation - previous studies have focused on populationlevel analyses, revealing systematic errors in estimating the travelled angles and distances. However, at the individual level, there are indications that people also possess left or right biases that are classically overlooked when pooling left and right trials. Therefore, we carefully investigate individual path integration errors in (1) a re-analysis of data from several influential human navigation studies, and (2) our own virtual reality path integration experiment. For both, we confirm time-persistent individual side biases, but find no evidence for consistent errors at the population level, suggesting that important aspects in human navigation performance might be overlooked by averaging across sides.

animal behavior and cognition↗

bioRxiv2025

Mobile Eye Tracking in the Real World: Best Practices

As research on human behavior, such as spatial navigation, increasingly adopts naturalistic settings, establishing best practices for such experiments becomes essential. While virtual reality (VR) offers a bridge between laboratory control and real-world complexity, it does not fully capture the experiential richness of real-world environments. Here, we present a demonstration of a mobile eye-tracking study conducted in a large-scale, outdoor urban environment, featuring unconstrained, long-duration free exploration and outside-pointing tasks. Using the city of Limassol, Cyprus as our testbed, we showcase the feasibility of collecting high-quality mobile eye-tracking, head orientation, and GPS data "in the wild," capturing a wide range of natural behavior with minimal experimental constraints. Based on this experience, we provide a set of best practices tailored to the logistical and methodological challenges posed by complex, real-world urban settings, challenges unlikely to arise in traditional indoor or highly controlled environments. While these recommendations have general relevance, we exemplify them in the context of spatial navigation research. By establishing methodological standards for studies at this scale, we aim to encourage and inform future research into naturalistic human behavior outside the laboratory.

neuroscience↗

bioRxiv2025

Expression of human CEACAMs promotes inflammation and organ damage during systemic Candida albicans infection in mice

Invasive candidiasis is a fungal infection characterized by a high mortality rate. CEACAM family receptors play a crucial role in regulating innate responses of both leukocytes and epithelia. Human CEACAM3, CEACAM5 and CEACAM6 receptors recognize C. albicans and are expressed in transgenic CEABAC10 mice. In a murine C. albicans infection model, CEABAC10 mice exhibited a shortened survival period attributed to an early cytokine storm, an exacerbated acute phase response, and heightened systemic inflammation compared to their wild-type littermates. The livers and kidneys of CEABAC10 mice displayed intensified purulent necrotizing inflammation, accompanied by increased infiltration of neutrophils and macrophages. Our in vivo and in vitro data indicated that the expression of CEACAM6 on monocytes of CEABAC10 mice caused the elevated cytokine levels and the subsequent exacerbation of the acute phase response upon C. albicans infection, resulting in decreased survival.

immunology↗

bioRxiv2023

The role of pneumococcal extracellular vesicles on the pathophysiology of the kidney disease Hemolytic Uremic Syndrome

Streptococcus pneumoniae-induced hemolytic uremic syndrome (Sp-HUS) is a kidney disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, and acute kidney injury. This disease is frequently underdiagnosed and its pathophysiology is poorly understood. In this work, we compared clinical strains, isolated from infant Sp-HUS patients, to a reference pathogenic strain D39, for host cytotoxicity and further explored the role of Sp-derived extracellular vesicles (EVs) in the pathogenesis of a HUS infection. In comparison with the WT strain, pneumococcal HUS strains caused significant lysis of human erythrocytes and increased the release of hydrogen peroxide. Isolated Sp-HUS EVs were characterized by performing dynamic light-scattering microscopy and proteomic analysis. Sp-HUS strain released EVs at a constant concentration during growth, yet the size of the EVs varied and several subpopulations emerged at later time points. The cargo of the Sp-HUS EVs included several virulence factors at high abundance, i.e., the ribosomal subunit assembly factor BipA, the Pneumococcal Surface Protein A (PspA), the lytic enzyme LytC, several sugar utilization and fatty acid synthesis proteins. Sp-HUS EVs strongly downregulated the expression of the endothelial surface marker PECAM-1 and were internalized by human endothelial cells. Sp-HUS EVs elicited the release of pro-inflammatory cytokines (IL-1{beta}, IL-6) and chemokines (CCL2, CCL3, CXCL1) by human monocytes. These findings shed new light on the overall function of Sp-EVs, in the scope of infection-mediated HUS, and suggest new avenues of research for exploring the usefulness of Sp-EVs as therapeutic and diagnostic targets. ImportanceStreptococcus pneumoniae is a life-threatening human pathogen associated with severe illnesses in the upper respiratory tract. Disseminated infections also occur, as the kidney disease hemolytic uremic syndrome. Even though vaccination is available, this pathogen is responsible for a worldwide high mortality rate, especially among children from least developed countries, where vaccination strategies are poor or inexistent. It is estimated that 30% of invasive pneumococcal diseases are caused by antibiotic resistant bacteria, leading to the classification of "serious threat" by the World Health Organization. In order to prevent cases of severe illness, investigation in the direction of new vaccine candidates is of upmost importance. Pneumococcal extracellular vesicles pose as ideal candidates for a serotype-independent vaccine formulation. To this purpose, the aspects of vesicle formation, cargo allocation and function need to be understood in detail. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/526387v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1f5faeborg.highwire.dtl.DTLVardef@2c6176org.highwire.dtl.DTLVardef@1b29245org.highwire.dtl.DTLVardef@a119ea_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗