Biology subjects

Muller, H.

Publications and source records attributed to Muller, H..

16 recordsLinked to original sources

bioRxiv2026

CD47 blockade augments anti-GD2 driven phagocytosis in vitro but fails to improve in vivo efficacy in immune competent, chemoresistant neuroblastoma preclinical models

CD47 delivers a dominant "Dont Eat Me" signal that inhibits macrophage-mediated clearance of tumour cells. Using immune competent, chemoresistant neuroblastoma (NB) models, we tested a Fc-silent CD47 blocker (ALX301) with anti-GD2 antibody alone and in combination with a clinically aligned temozolomide/irinotecan chemoimmunotherapy backbone. Tumours expressed GD2 and CD47, and bound ALX301. In macrophage coculture assays, anti-GD2 antibody induced dose-dependent phagocytosis, whereas ALX301 or an anti-CD47 antibody alone did not. CD47 blockade in combination with a suboptimal concentration of anti-GD2 antibody showed an additive effect on phagocytosis in vitro. In vivo, however, ALX301 failed to improve tumour control or survival when added to anti-GD2 or to chemoimmunotherapy in two models. Toxicity was acceptable, showing only mild, expected red-cell changes without organ injury. This form of CD47 inhibition is therefore mechanistically active in vitro but insufficient to enhance anti-GD2 antibody-based therapy in immune competent mice bearing a chemoresistant NB, highlighting the potential need for myeloid-reprogramming partners.

immunology↗

bioRxiv2024

Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals

Horizontal transfer of transposable elements (HTT) is an important driver of genome evolution, yet the factors conditioning this phenomenon remain poorly characterized. Here, we screened 247 animal genomes from four phyla (annelids, arthropods, mollusks, chordates), spanning 19 independent transitions between aquatic and terrestrial lifestyles, to evaluate the suspected positive effects of aquatic habitat and of phylogenetic relatedness on HTT. Among the 5,952 independent HTT events recovered, the vast majority (>85%) involve DNA transposons, of which Mariner-like and hAT-like elements have the highest rates of horizontal transfer, and of intra-genomic amplification. Using a novel approach that circumvents putative biases linked to phylogenetic inertia and taxon sampling, we found that HTT rates positively correlate with similarity in habitat type but were not significantly higher in aquatic than in terrestrial animals. However, modelling the number of HTT events as a function of divergence time in a Bayesian framework revealed a clear positive effect of phylogenetic relatedness on HTT rates in most of the animal species studied (162 out of 247). The effect is very pronounced: a typical species is expected to show 10 times more transfers with a species it diverged from 125 million years (My) ago than with a species it diverged from 375 My ago. Overall, our study underscores the pervasiveness of HTT throughout animals and the impact of evolutionary relatedness on its dynamics. Significance statementGenetic material can be transmitted between organisms through other means than reproduction, in a process called horizontal transfer. The mechanisms and factors underlying this phenomenon in animals remain unclear, although it often involves transposable elements (TEs). TEs are DNA segments capable of jumping within genomes, but also occasionally between individuals. Here, we show evidence for nearly 6,000 transfers of TEs among animals, based on genomic comparisons among 247 species of annelids, arthropods, chordates and mollusks. Contrarily to expectations, we found no excess in the rates of transfers in aquatic versus terrestrial animals. By contrast, most analyzed species appeared engaged in many more horizontal transfers with close than with distant relatives, highlighting the strong impact of phylogenetic relatedness on horizontal transfers of TEs.

evolutionary biology↗

bioRxiv2024

Dissociation of movement and outcome representations in metacognition of agency

We studied the role of movement and outcome information in forming metacognitive representations of agency. Participants completed a goal-oriented task, a virtual version of a ball-throwing game. In two conditions, we manipulated either the visual representation of the throwing movement or its distal outcome (the resulting ball flight/trajectory). We measured participants accuracy in a discrimination agency task, as well as confidence in their responses and tested for differences in the electrophysiological (EEG) signal using linear mixed effect models. We found no mean differences between participants metacognitive efficiency between conditions, but we also found that metacognitive sensitivity did not correlate between the two conditions, suggesting a dissociation in their underlying mechanisms. Furthermore, exploratory analyses pointed toward a difference in the EEG signal between the two conditions. Taken together, our results suggest that while movement and outcome information contribute equally to participants sense of agency, they may do so through distinct underlying processes.

neuroscience↗

bioRxiv2024

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

genomics↗

bioRxiv2024

Blocking MIF secretion enhances CAR T-cell efficacy against neuroblastoma

While chimeric antigen receptor (CAR) T-cell therapies are showing highly promising first results in neuroblastoma, immunosuppressive tumor microenvironments (TME) limit T cell persistence and durable clinical efficacy. To improve CAR T-cell efficacy further, we applied a multi-omics approach including single-cell RNA sequencing and proteomics, which identified 13 targetable immunosuppressive factors in neuroblastoma. Of these, macrophage migration inhibitory factor (MIF) and midkine (MDK) were validated across multiple published RNA datasets. Moreover, they were secreted in high abundance by neuroblastoma tumoroids. Functional validation experiments revealed MIF as a potent inhibitor of CAR T-cells, in vitro and in vivo. Degradation of MIF by PROTAC technology significantly enhanced CAR T-cell activation targeting GPC2 and B7-H3, providing a potential intervention against MIF. By defining the immunosuppressive effects of neuroblastomas TME on CAR T-cell efficacy, particularly the pivotal role of MIF, we provide a therapeutic strategy for improving adoptive cell therapies for this pediatric malignancy.

cancer biology↗

bioRxiv2024

Functional avidity of anti-B7H3 CAR-T constructs predicts antigen density thresholds for triggering effector function

Chimeric Antigen receptor T cell (CAR-T) treatments for solid cancers have been compromised by limited expansion and survival in the tumor microenvironment following interaction with antigen-expressing target cells. Using B7H3 as a model antigen with broad clinical applicability, we evaluated the relationship between the antibody/antigen affinity of three clinical candidate binders and the three following functional characteristics: functional avidity, prolonged cytotoxicity in tumoroid re-stimulation assays, and in vivo anti-tumoral responses. BEHAV3D video-microscopy assessed distinct CAR-T cell behaviors at single cell resolution. T cell exhaustion did not dictate effector function. Rather, we demonstrated a threshold avidity of CAR-T / tumor cell interaction, characterized by longer cumulative CD8+ CAR-T / tumor target interaction times, and required for adequate CAR-T cell expansion to result in sustained tumor control upon re-challenge. These results provide new insights into design of CAR-T cells for antigen-dim cell targeting, and avoidance of antigen-dim tumor relapse.

bioengineering↗

bioRxiv2024

Localising elements in single-particle reconstructions by REEL-EM: Reconstructed Electron Energy-Loss - Elemental Mapping

For structures determined by single particle cryo-EM, no technique currently exists for mapping elements to defined locations, leading to errors in the assignment of metals and other ions, cofactors, substrates, inhibitors, and lipids that play essential roles in activity and regulation. Elemental mapping in the electron microscope is well established for dose-tolerant samples but is challenging for biological samples, especially in a cryo-preserved state. Here, we combine electron energy-loss spectroscopy (EELS) with single-particle image processing to allow elemental mapping in cryo-preserved macromolecular complexes. Proof-of-principle data show that our method, REEL-EM, allows 3D reconstruction of EELS data, such that a high total electron dose is accumulated across many copies of a complex. Working with two test samples, we demonstrate that we can reliably localise abundant elements. We discuss the current limitations of the method and potential future developments.

biophysics↗

bioRxiv2023

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori

Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these are mainly observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is "secluded" from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. Polymer simulations show that this contact pattern can only be explained by high loop-extrusion activity within compartment S, combined with low extrusion elsewhere through the genome. This unique, targeted extrusion represents a novel phenomenon and underscores how evolutionarily conserved mechanisms--compartmentalization and loop extrusion--can be repurposed to create new 3D genome architectures.

genomics↗

bioRxiv2022

Somatic chromosomal integration of polydnavirus during parasitism triggered their germline infiltration in multiple lepidopteran families

Increasing numbers of horizontal transfer (HT) of genes and transposable elements are reported in insects. Yet the mechanisms underlying these transfers remain unknown. Here we firs t quantify and characterize the patterns of chromosomal integration of the polydnavirus (PDV) encoded by the Campopleginae Hyposoter didymator parasitoid wasp (HdIV) in somatic cells of parasitized fall armyworm (Spodoptera frugiperda). Polydnaviruses are domesticated viruses injected by wasps together with their eggs into their hosts in order to facilitate the development of wasp larvae. We found that six HdIV DNA circles integrate into the genome of host somatic cells. Each host haploid genome suffers between 23 and 40 integration events (IEs) on average 72 hours post parasitism. Almost all IEs are mediated by DNA double strand breaks occurring in the host integration motif (HIM) of HdIV circles. We show that despite their independent evolutionary origins, PDV from both Campopleginae and Braconidae wasps use remarkably similar mechanisms for chromosomal integration. Next, our similarity search performed on 775 genomes reveals that PDVs of both Campopleginae and Braconidae wasps have recurrently colonized the germline of dozens of lepidopteran species through the same mechanisms they use to integrate into somatic host chromosomes during parasitism. We found evidence of HIM-mediated HT of PDV DNA circles in no less than 124 species belonging to 15 lepidopteran families. Thus, this mechanism underlies a major route of HT of genetic material from wasps to lepidopterans with likely important consequences on lepidopterans.

evolutionary biology↗

bioRxiv2022

Motor outcomes congruent with intentions may sharpen metacognitive representations

We can monitor our intentional movements, in order to describe how we move our bodies. But it is unclear which information this metacognitive monitoring relies on. For example, when throwing a ball to hit a target, we might use the visual information about how the ball flew to metacognitively assess our performance. Alternatively, we might disregard the ball trajectory -- given that it is not directly relevant to our goal -- and metacognitively assess our performance based solely on whether we reached the goal of hitting the target. In two experiments we aimed to distinguish between these two alternatives and asked whether the distal outcome of a goal-directed action (hitting or missing a target) informs the metacognitive representations of our own movements. Participants performed a semi-virtual task where they moved their arm to throw a virtual ball at a target. After each throw, participants discriminated which of two ball trajectories displayed on the screen corresponded to the flight path of their throw and then rated their confidence in this decision. The task included two conditions that differed on whether the distal outcome of the two trajectories shown matched (congruent) or differed (incongruent). Participants were significantly more accurate in discriminating between the two trajectories, and responded faster in the incongruent condition and, accordingly, were significantly more confident on these trials. Crucially, we found significant differences in metacognitive performance (measured as meta-d/d) between the two conditions only on successful trials, where the virtual ball had hit the target. These results indicate that participants successfully incorporated information about the outcome of the movement into both their discrimination and confidence responses. However, information about the outcome selectively sharpened the precision of confidence ratings only when the outcome of their throw matched their intention. We argue that these findings underline the separation between the different levels of information that may contribute to body monitoring, and we provide evidence that intentions might play a central role in metacognitive motor representations. HighlightsO_LIParticipants threw a virtual ball to hit a target C_LIO_LIFollowing their throw participants selected between two plausible trajectories C_LIO_LIOn half the trials, the two alternative trajectories differed in their distal outcome. C_LIO_LIDiscrimination and confidence were higher in trials with different outcome. C_LIO_LIMetacognitive performance was best in hit trials when the alternative missed. C_LI

neuroscience↗

bioRxiv2021

αB-crystallin affects the morphology of Aβ(1-40) aggregates

B-crystallin (ABC) is a human small heat shock protein that is strongly linked to Alzheimers disease (AD). In vitro, it can inhibit the aggregation and amyloid formation of a range of proteins including A{beta}(1-40), a primary component of AD amyloid plaques. Despite the strong links, the mechanism by which ABC inhibits amyloid formation has remained elusive, in part due to the notorious irreproducibility of aggregation assays involving preparations of A{beta}-peptides of native sequence. Here, we present a recombinant expression protocol to produce native A{beta}(1-40), devoid of any modifications or exogenous residues, with yields up to 4 mg/L E. coli. This material provides highly reproducible aggregation kinetics and, by varying the solution conditions, we obtain either highly ordered amyloid fibrils or more disordered aggregates. Addition of ABC slows the aggregation of A{beta}(1-40), and interferes specifically with the formation of ordered amyloid fibrils, favouring instead the more disordered aggregates. Solution-state NMR spectroscopy reveals that the interaction of ABC with A{beta}(1-40) depends on the specific aggregate morphology. These results provide mechanistic insight into how ABC inhibits the formation of amyloid fibrils. HighlightsO_LIProtocol for production of native recombinant A{beta}(1-40) C_LIO_LIAmyloid formation under physiological conditions is highly reproducible C_LIO_LIBoth ordered fibrils and disordered aggregates can be reliably formed C_LIO_LIB-crystallin specifically inhibits amyloid fibril assembling, favouring disordered aggregates C_LI eTOC blurbMuller et al. introduce a protocol for the highly reproducible production of amyloid from native A{beta}(1-40) and determine that the human chaperone ABC specifically destabilises them in favour of disordered aggregates. NMR shows that ABC can distinguish between aggregate morphologies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/433908v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@fe31fborg.highwire.dtl.DTLVardef@8367aforg.highwire.dtl.DTLVardef@10c42a3org.highwire.dtl.DTLVardef@1eaddeb_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Label-free optical detection of bioelectric potentials using electrochromic thin films

Understanding how a network of interconnected neurons receives, stores, and processes information in the human brain is one of the outstanding scientific challenges of our time. The ability to reliably detect neuroelectric activities is essential to addressing this challenge. Optical recording using voltage-sensitive fluorescent probes has provided unprecedented flexibility for choosing regions of interest in recording neuronal activities. However, when recording at a high frame rate such as 500-1000 Hz, fluorescence-based voltage sensors often suffer from photobleaching and phototoxicity, which limit the recording duration. Here, we report a new approach, Electro-Chromic Optical REcording (ECORE), that achieves label-free optical recording of spontaneous neuroelectrical activities. ECORE utilizes the electrochromism of PEDOT:PSS thin films, whose optical absorption can be modulated by an applied voltage. Being based on optical reflection instead of fluorescence, ECORE offers the flexibility of an optical probe without suffering from photobleaching or phototoxicity. Using ECORE, we optically recorded spontaneous action potentials in cardiomyocytes, cultured hippocampal and dorsal root ganglion neurons, and brain slices. With minimal perturbation to cells, ECORE allows long-term optical recording over multiple days.

neuroscience↗

bioRxiv2018

Deep learning based retrieval system for gigapixel histopathology cases and open access literature

Clinical practice is getting increasingly stressful for pathologists due to increasing complexity and time constraints. Histopathology is slowly shifting to digital pathology, thus creating opportunities to allow pathologists to improve reading quality or save time using Artificial Intelligence (AI)-based applications. We aim to enhance the practice of pathologists through a retrieval system that allows them to simplify their workflow, limit the need for second opinions, while also learning in the process. In this work, an innovative retrieval system for digital pathology is integrated within a Whole Slide Image (WSI) viewer, allowing to define regions of interest in images as queries for finding visually similar areas using deep representations. The back-end similarity computation algorithms are based on a multimodal approach, allowing to exploit both text information and content-based image features. Shallow and deep representations of the images were evaluated, the later showed a better overall retrieval performance in a set of 112 whole slide images from biopsies. The system was also tested by pathologists, highlighting its capabilities and suggesting possible ways to improve it and make it more usable in clinical practice. The retrieval system developed can enhance the practice of pathologists by enabling them to use their experience and knowledge to properly control artificial intelligence tools for navigating repositories of images for decision support purposes.

pathology↗

bioRxiv2018

Glucocerebrosidase rescues alpha-synuclein from amyloid formation

Aggregation of the protein -synuclein (Syn) Into amyloid fibrils is associated with Parkinsons disease (PD), a process accelerated by lipids. Recently, the lysosomal protein glucocerebrosidase (GCase) has been identified as a major risk factor in both genetic and sporadic PD. Here, we use solution state NMR to reveal that GCase directly inhibits lipid induced Syn amyloidogenesis. Structurally, we show that the mechanism for this requires competition between lipids and GCase for Syn, binding the N and C termini respectively. The affinity of GCase for the C-terminus of Syn is such that not only does it inhibit lipid induced amyloid formation, but also it destabilizes mature Syn amyloid fibrils. These results reveal a competitive molecular \"tug-of-war\" for Syn termini by GCase and lipid, providing a mechanistic link between the clinically observed links between changes in GCase abundance and Parkinsons disease.

biophysics↗

bioRxiv2017

Redesigning chromosomes to optimize conformation capture (Hi-C) assays

In all chromosome conformation capture based experiments the accuracy with which contacts are detected varies considerably because of the uneven distribution of restriction sites along genomes. In addition, repeated sequences as well as homologous, large identical regions remain invisible to the assay because of the ambiguities they introduce during the alignment of the sequencing reads along the genome. As a result, the investigation of homologs during meiosis prophase through 3C studies has been limited. Here, we redesigned and reassembled in yeast a 145kb region with regularly spaced restriction sites for various enzymes. Thanks to this Syn-3C design, we enhanced the signal to noise ratio and improved the visibility of the entire region. We also improved our understanding of Hi-C data and definition of resolution. The redesigned sequence is now distinguishable from its native homologous counterpart in an isogenic diploid strain. As a proof of principle, we track the establishment of homolog pairing during meiotic prophase in a synchronized population. This provides new insights on the individualization and pairing of homologs, as well as on their internal restructuration into arrays of loops during meiosis prophase. Overall, we show the interest of redesigned genomic regions to explore complex biological questions otherwise difficult to address.

synthetic biology↗

bioRxiv2016

Choreography of budding yeast chromosomes during the cell cycle

To ensure the proper transmission of the genetic information, DNA molecules must be faithfully duplicated and segregated. These processes involve dynamic modifications of chromosomes internal structure to promote their individualization, as well as their global repositioning into daughter cells (Guacci et al., 1994; Kleckner et al., 2014; Mizuguchi et al., 2014). In eukaryotes, these events are regulated by conserved architectural proteins, such as structural maintenance of chromosomes (SMC i.e. cohesin and condensin) complexes (Aragon et al., 2013a; Uhlmann, 2016). Although the roles of these factors have been actively investigated, the genome-wide chromosomal architecture and dynamics both at small and large-scales during cell division remains elusive. Here we report a comprehensive Hi-C (Dekker et al., 2002; Lieberman-Aiden et al., 2009) analysis of the dynamic changes of chromosomes structure over the Saccharomyces cerevisiae cell cycle. We uncover specific SMC-dependent structural transitions between the different phases of the mitotic cycle. During replication, cohesion establishment promotes the increase of long-range intra-chromosomal contacts. This process correlates with the individualization of chromosomes, which culminates at metaphase. Mitotic chromosomes are then abruptly reorganized in anaphase by the mechanical forces exerted by the mitotic spindle on the centromere cluster. The formation of a condensin-dependent loop, that bridges centromere cluster with the cenproximal flanking region of the rDNA, suggests that these forces may directly facilitate nucleolus segregation. This work provides a comprehensive overview of chromosome dynamics during the cell cycle of a unicellular eukaryote that recapitulates and unveils new features of highly conserved stages of the cell division.

genetics↗