Biology subjects

Müller, N.

Publications and source records attributed to Müller, N..

6 recordsLinked to original sources

bioRxiv2026

Brain alignment in deep neural networks emerges early and independently of object classification

Deep convolutional neural networks are leading models of biological vision, largely because of their strong brain alignment: their features predict neural responses better than earlier models. Yet they are believed to recognize objects differently, relying on texture where humans rely on shape and failing on perturbations humans handle effortlessly. What then does alignment reflect? Tracking three architectures densely during training, we find that alignment with human fMRI, EEG, and macaque electrophysiology is already largely present at initialization, when networks classify at chance, and reaches a plateau within one to five epochs; thereafter it changes only modestly while classification accuracy continues to climb to 75%. Network lesioning shows that a kernel's contribution to alignment is essentially uncorrelated with its contribution to classification throughout training. Brain-network alignment therefore appears to reflect the structure of the visual environment both systems encode, rather than a shared solution for classification.

neuroscience↗

bioRxiv2026

Learning to See Like a Child: Why Viewpoint Diversity is Fundamental for Human-Aligned Object Recognition

Deep convolutional neural networks match human accuracy on standard object recognition tasks but fail to recognize familiar objects from novel view-points. Humans, however, develop viewpoint-invariant recognition at an early age through diverse visual experience. This gap in visual experience may explain why models diverge from humans in object recognition. Holding dataset size constant, we show that greater viewpoint diversity substantially improves generalization to novel views. Using a synthetic 3D dataset with systematically controlled viewpoints, we reveal a core trade-off: restricted-view training yields rapid learning and near-ceiling in-distribution accuracy but collapses on held-out viewpoints, whereas viewpoint-diverse training learns more gradually yet generalizes robustly. Increasing viewpoint diversity disrupts texture regularities while preserving global shape, driving networks to prioritize shape over texture - the same strategy that underlies human object recognition. Partitioned Grad-CAM analyses further show that viewpoint-diverse models maintain object-centered attention. These findings parallel developmental accounts of multi-view learning and identify viewpoint diversity as an important factor for robust, human-aligned vision.

neuroscience↗

bioRxiv2022

Single- and duplex TaqMan-quantitative PCR for determining the copy numbers of integrated selection markers during site-specific mutagenesis in Toxoplasma gondii by CRISPR-Cas9

Herein, we developed a single and a duplex TaqMan quantitative qPCR for absolute quantification of copy numbers of integrated dihydrofolate reductase-thymidylate synthase (mdhfr-ts) drug selectable marker for pyrimethamine resistance in Toxoplasma gondii knockouts (KOs). The single TaqMan qPCR amplifies a 174 bp DNA fragment of the inserted mdhfr-ts and of the wild-type (WT) dhfr-ts (wt-dhfr-ts) which is present as single copy gene in Toxoplasma and encodes a sensitive enzyme to pyrimethamine. Thus, the copy number of the dhfr-ts fragment in a given DNA quantity from KO parasites with a single site-specific integration should be twice the number of dhfr-ts copies recorded in the same DNA quantity from WT parasites. The duplex TaqMan qPCR allows simultaneous amplification of the 174 bp dhfr-ts fragment and the T. gondii 529-bp repeat element. Accordingly, for a WT DNA sample, the determined number of tachyzoites given by dhfr-ts amplification is equal to the number of tachyzoites determined by amplification of the Toxoplasma 529-bp, resulting thus in a ratio of 1. However, for a KO clone having a single site-specific integration of mdhfr-ts, the calculated ratio is 2. We then applied both approaches to test T. gondii RH mutants in which the major surface antigen (SAG1) was disrupted through insertion of mdhfr-ts using CRISPR-Cas9. Results from both assays were in correlation showing a high accuracy in detecting KOs with multiple integrated mdhfr-ts. Southern blot analyses using BsaBI and DraIII confirmed qPCRs results. Both TaqMan qPCRs are needed for reliable diagnostic of T. gondii KOs following CRISPR-Cas9-mediated mutagenesis, particularly with respect to off-target effects resulting from multiple insertions of mdhfr-ts. The principle of the duplex TaqMan qPCR is applicable for other selectable markers in Toxoplasma. TaqMan qPCR tools may contribute to more frequent use of WT Toxoplasma strains during functional genomics.

molecular biology↗

bioRxiv2021

Trypanosome morphogenesis involves recruitment of a pleckstrin homology domain protein by an orphan kinesin to the microtubule quartet

Kinesins are motor proteins found in all eukaryotic lineages that move along microtubules to mediate cellular processes such as mitosis and intracellular transport. In trypanosomatids, the kinesin superfamily has undergone a prominent expansion, resulting in one of the most diverse kinesin repertoires that includes the two kinetoplastid-restricted families X1 and X2. Here, we characterize in Trypanosoma brucei TbKifX2A, an orphaned X2 kinesin. TbKifX2A tightly interacts with TbPH1, a kinesin-like protein with a likely inactive motor domain, a rarely reported occurrence. Both TbKifX2A and TbPH1 localize to the microtubule quartet (MtQ), a characteristic but poorly understood cytoskeletal structure that wraps around the flagellar pocket as it extends to the cell body anterior. The proximal proteome of TbPH1 revealed two other interacting proteins, the flagellar pocket protein FP45 and intriguingly another X2 kinesin, TbKifX2C. Simultaneous ablation of TbKifX2A/TbPH1 results in the depletion of FP45 and TbKifX2C and also an expansion of the flagellar pocket, among other morphological defects. TbKifX2A is the first motor protein to be localized to the MtQ. The observation that TbKifX2C also associates with the MtQ suggests that the X2 kinesin family may have co-evolved with the MtQ, both kinetoplastid-specific traits.

molecular biology↗

bioRxiv2019

In vitro model for resistance in oncogene-dependent tumors at the limit of radiological detectability

In solid tumors, the response to targeted therapy is typically short-lived, as therapy-resistant mutants can quickly expand during therapy. Here we analyze the spectrum of such resistance mutations coexisting in a large population of cancer cells. We use an iterative scheme of artificial evolution to amplify and isolate different resistance mechanisms. As a proof of concept, we apply our scheme to PC-9 cells, a human non-small cell lung cancer cell line with an activating EGFR mutation. The mechanisms we find comprise the well-known gatekeeper-mutation T790M in EGFR, a mutation in NRAS, the amplification of MET-ligand HGF, as well as induction of AKT-mTOR signaling. In this model, a combination of four drugs targeting these mechanisms prevents not only the expansion of resistant cells, but also inhibits the growth of drug-tolerant cells, which can otherwise act as a reservoir for further resistance mutations. These data suggest that a finite number of drugs specifically acting on individual resistant clones may be able to control resistance in oncogenically driven lung cancer.

cancer biology↗

bioRxiv2019

SiaABCD - A threonine phosphorylation pathway that controls biofilm formation in Pseudomonas aeruginosa

The critical role of bacterial biofilms in chronic human infections calls for novel anti-biofilm strategies targeting the regulation of biofilm development. However, the regulation of biofilm development is very complex and can include multiple, highly interconnected signal transduction/response pathways, which are incompletely understood. We demonstrated previously that in the opportunistic, human pathogen P. aeruginosa, the PP2C-like protein phosphatase SiaA and the di-guanylate cyclase SiaD control the formation of macroscopic cellular aggregates, a type of suspended biofilms, in response to surfactant stress. In this study, we demonstrate that the SiaABC proteins represent a signal response pathway that functions through a partner switch mechanism to control biofilm formation. We also demonstrate that SiaABCD functionality is dependent on carbon substrate availability for a variety of substrates, and that upon carbon starvation, SiaB mutants show impaired dispersal, in particular with the primary fermentation product ethanol. This suggests that carbon availability is at least one of the key environmental cues integrated by the SiaABCD system. Further, our biochemical, physiological and crystallographic data reveals that the phosphatase SiaA and its kinase counterpart SiaB balance the phosphorylation status of their target protein SiaC at threonine 68 (T68). Crystallographic analysis of the SiaA-PP2C domain shows that SiaA is present as a dimer. Dynamic modelling of SiaA with SiaC suggested that SiaA interacts strongly with phosphorylated SiaC and dissociates rapidly upon dephosphorylation of SiaC. Further, we show that the known phosphatase inhibitor fumonisin inhibits SiaA mediated phosphatase activity in vitro. In conclusion, the present work improves our understanding of how P. aeuruginosa integrates specific environmental conditions, such as carbon availability and surfactant stress, to regulate cellular aggregation and biofilm formation. With the biochemical and structural characterization of SiaA, initial data on the catalytic inhibition of SiaA, and the interaction between SiaA and SiaC, our study identifies promising targets for the development of biofilm-interference drugs to combat infections of this aggressive opportunistic pathogen. Author SummaryPseudomonas aeruginosa is a Gram-negative bacterium that is feared within clinical environments due to its potential to cause life-threatening acute and chronic infections. One cornerstone of its success is the ability to form and disperse from biofilms, which are self-made, multicellular structures that protect the individual cell from the human immune system and antibiotic treatment. As such, therapies that combine a biofilm-interference strategy and the use of antimicrobial drugs represent one of the promising strategies to tackle infections of this organism. With the current study, we gain a deeper understanding of the SiaABCD mediated biofilm formation in response to clinically relevant environmental conditions. Further, our structural and biochemical characterization of the PP2C-type protein-phosphatase SiaA and the partner switch protein SiaC suggest that both represent promising novel targets for the development of future anti-biofilms drugs based on a signal interference strategy.

microbiology↗