Biology subjects

Timm, J.

Publications and source records attributed to Timm, J..

11 recordsLinked to original sources

bioRxiv2026

CMV Replication Drives IFNγ-Mediated Sensitization of AML Cells to Cytotoxic Killing Through the NKG2C-HLA-E Axis

Human cytomegalovirus (CMV) infection represents a significant risk factor for transplant recipients, including patients undergoing hematopoietic stem cell transplantation (HSCT). Interestingly, several studies have reported an association between early CMV reactivation and a reduced risk of leukemia relapse, particularly in acute myeloid leukemia (AML). Given that CMV profoundly shapes the natural killer (NK) cell compartment, a contribution of CMV-primed NK cells to this effect has been proposed. To explore this mechanism, we analyzed the relationship between NK cell functionality and CMV reactivation in the context of AML. Consistent with observations in peripheral blood, CMV-seropositive HSCT recipients displayed expanded NKG2Cpos NK cell populations within the bone marrow, characterized by high Granzyme B expression. CMV replication was associated with elevated plasma IFN{gamma} levels, which in vitro rendered AML cells more susceptible to apoptosis when co-cultured with peripheral blood mononuclear cells. Importantly, IFN{gamma} treatment modulated NK cell responses by inducing a variety of NK cell ligands including HLA-E on primary bone marrow-derived blasts and AML cell lines. In line with this, the activation of CMV-associated NKG2Cpos NK cells was enhanced upon stimulation with IFN{gamma}-pretreated AML cells. In summary, our findings demonstrate that CMV replication induces a transient increase in IFN{gamma} levels that influences both AML and NK cells, ultimately enhancing AML cell susceptibility to NK cell-mediated cytotoxicity initiated through the NKG2C-HLA-E axis. ImportancePrevious studies suggested that CMV reactivation after HSCT may reduce leukemia relapse in AML patients, but the underlying mechanism remained unclear. Here, we show that CMV replication induces IFN{gamma} release, which sensitizes AML cells to NK cell-mediated killing. This effect involves upregulation of HLA-E on AML cells and activation of expanded NKG2Cpos NK cells within the bone marrow. Our findings uncover a novel IFN{gamma}-dependent link between CMV replication and enhanced NK cell cytotoxicity in AML, suggesting that combining IFN{gamma} treatment with NK cell-based immunotherapy or NKG2A blockade could reduce post-HSCT relapse, even in CMV-negative patients.

immunology↗

bioRxiv2025

Distributed burst activity in the thalamocortical system encodes reward contingencies during learning

Neuronal bursts are distinct high-frequency firing patterns that are present ubiquitously throughout mammalian brain circuits. Although bursts are considered part of a universal neural code, the information they convey has long been a subject of debate. In this study, we investigated neuronal activity in simultaneously recorded regions of the thalamocortical system in freely moving mice as they learned stimulus-outcome associations in a go/no-go task. We discovered that, in parallel with learning, populations of neurons emerge in cortical, thalamic, and extrathalamic regions of the somatosensory system that encode task-relevant stimulus features via the presence or absence of bursts. These burst-coder neurons (BCNs) increase in number with task proficiency and exhibit burstiness that scales with stimulus valence rather than physical stimulus identity. Notably, BCNs consistently track stimulus-outcome associations--even after multiple rule switches--by inverting their burst encoding of the physical stimuli, indicating that burst coding is driven by outcome associations rather than by inherent stimulus properties. Although burst coding emerges throughout the thalamocortical system, only cortical units retain significant burst coding after devaluation, while other regions lose their discriminative burst patterns. Furthermore, decoding of stimulus properties and behavior achieves maximal accuracy when bursts or BCNs are used as input. Overall, these results provide direct experimental evidence linking neuronal bursting to learning, supporting a novel perspective of bursts as context encoders and teaching signals.

neuroscience↗

bioRxiv2024

A tactile discrimination task to study neuronal dynamics in freely-moving mice

Sensory discrimination tasks are valuable tools to study neuronal mechanisms of perception and learning. Most discrimination tasks for electrophysiological and imaging studies in rodents require the animals to be head-fixed. However, implementing neurophysiological recordings into more ethologically realistic settings with unrestrained animals has been challenging. Here, we introduce a whisker-dependent discrimination task for freely moving mice, integrating electrophysiology and calcium imaging with cellular resolution. In this go/no-go paradigm, male mice learned to discriminate aperture widths within days while foraging on a linear platform. The setups versatility enables exploration into diverse behavioral aspects, including tactile discrimination thresholds, valence-dependent behavior, and cognitive flexibility following repeated task rule reversals. Rule learning was highly stereotypical, fast and reproducible across individual mice. Electrophysiological recordings revealed distributed tactile processing across the thalamocortical system, with subsets of units encoding both movement- and stimulus-related features. Sensory encoding was strongly modulated by behavioral state, with neurons tuned to locomotion, whisking, whisker angle and phase, head angle, and spatial position. By enabling simultaneous extracellular recordings and calcium imaging within the same freely moving paradigm, this approach allows for precise synchronization of neural activity with multiple behavioral readouts. This paradigm provides a versatile tool to elucidate neural mechanisms of cognition and sensory processing in naturalistic conditions.

neuroscience↗

bioRxiv2022

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its [~]30 kb RNA genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11 polyprotein, whose mature products are cofactors of the viral replicase, identifying the order of cleavages as: 1) nsp9-10, 2) nsp8-9/nsp10-11, and 3) nsp7-8. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and X-ray scattering yielded three-dimensional models of the nsp7-10/11 polyprotein. Our data suggest that the nsp7- 10/11 structure in complex with Mpro strongly resembles the unbound polyprotein, and that both polyprotein conformation and junction accessibility determine the preference and order of cleavages. Finally, we used limited proteolysis assays to characterize the effect of a series of inhibitors/binders on Mpro processing of nsp7-11 and Mpro inhibition using a polyprotein substrate. TeaserWe elucidated the structural basis of order of cleavage of SARS-CoV-2 nsp7-11 polyprotein, with implications for Mpro inhibition.

biochemistry↗

bioRxiv2022

Design of a Minimal di-Nickel Hydrogenase Peptide

The most ancient processes for energy production in the evolution of life involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13 amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe]-hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase (ACS), two ancient, extant proteins central to metabolism. These experimental results clearly demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth. One Sentence SummarySmall metal-binding peptides were the likely precursors of modern enzymes.

biochemistry↗

bioRxiv2021

Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance

Third generation Hepatitis C virus (HCV) NS3/4A protease inhibitors (PIs), glecaprevir and voxilaprevir, are highly effective across genotypes and against many resistant variants. Unlike earlier PIs, these compounds have fluorine substitutions on the P2-P4 macrocycle and P1 moieties. Fluorination has long been used in medicinal chemistry as a strategy to improve physicochemical properties and potency. However, the molecular basis by which fluorination improves potency and resistance profile of HCV NS3/4A PIs is not well understood. To systematically analyze the contribution of fluorine substitutions to inhibitor potency and resistance profile, we used a multi-disciplinary approach involving inhibitor design and synthesis, enzyme inhibition assays, co-crystallography, and structural analysis. A panel of inhibitors in matched pairs were designed with and without P4 cap fluorination, tested against WT protease and the D168A resistant variant, and a total of 22 high-resolution co-crystal structures were determined. While fluorination did not significantly improve potency against the WT protease, PIs with fluorinated P4 caps retained much better potency against the D168A protease variant. Detailed analysis of the co-crystal structures revealed that PIs with fluorinated P4 caps can sample alternate binding conformations that enable adapting to structural changes induced by the D168A substitution. Our results elucidate molecular mechanisms of fluorine-specific inhibitor interactions that can be leveraged in avoiding drug resistance.

biochemistry↗

bioRxiv2021

HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations

MotivationA key process in anti-viral adaptive immunity is that the Human Leukocyte Antigen system (HLA) presents epitopes as Major Histocompatibility Complex I (MHC I) protein-peptide complexes on cell surfaces and in this way alerts CD8+ cytotoxic T-Lymphocytes (CTLs). This pathway exerts strong selection pressure on viruses, favoring viral mutants that escape recognition by the HLA/CTL system, e.g. by point mutations that decrease binding of viral peptides to MHC I. Naturally, such immune escape mutations often emerge in highly variable viruses, e.g. HIV or HBV, as HLA-associated mutations (HAMs), specific to the host HLA alleles and its MHC I proteins. The reliable identification of HAMs is not only important for understanding viral genomes and their evolution, but it also impacts the development of broadly effective anti-viral treatments and vaccines against variable viruses. By their very nature HAMs are amenable to detection by statistical methods in paired sequence / HLA data. However, HLA alleles are very polymorphic in the human host population which makes the available data relatively sparse and noisy. Under these circumstances, one way to optimize HAM detection is to integrate all relevant information in a coherent model. Bayesian inference offers a principled approach to achieve this. ResultsWe present a new regression model for the detection of HAMs. As we choose a Bayesian approach we can include the novel sparsity-inducing priors, and we obtain easily interpretable quantitative information on HAM candidates. The basic model can be extended to include prior information relevant to HAM detection, which we demonstrate by integrating predictions of epitope affinities to MHC I, predictions of epitope peptide processing, and computation of phylogenetic background. This integrative method improves performance in HAM detection considerably over state-of-the-art methods. AvailabilityThe source code of this software is available at https://github.com/HAMdetector/Escape.jl under a permissive MIT license. Contactdaniel.habermann@uni-due.de, daniel.hoffmann@uni-due.de

bioinformatics↗

bioRxiv2021

Strong genetic structure and limited connectivity among populations of Clark's Anemonefish (Amphiprion clarkii) in the centre of marine biodiversity

Populations of anemonefish species often show signs of local isolation due limited dispersal potential and oceanographic conditions. Additionally, anthropogenic pressure, such as overharvesting and coral reef exploitation causes reduced population size, eventually leading to local extinction. The understanding of the genetic population structure, as well as the influence of both historical and current connectivity, is required to design effective marine protected area (MPA) networks. In this study, the genetic structure of Clarks Anemonefish (Amphiprion clarkii) populations of the Indo-Malay Archipelago (IMA) is assessed through mitochondrial control region (mtCR) sequences and nuclear microsatellites. Results provided evidence of a significant genetic structure (mtCR: {Phi}st = 0.42039, {Phi}ct = 0.63852; microsatellites: Fst = 0.01449, Fct = 0.05199). Genetic breaks were identified among Western (Padang Karimunjawa), Central (Sulawesi, Borneo, Bali, Komodo, Timor), and Eastern (Biak) IMA populations, which matches with patterns obtained for congeneric and other coral reef taxa. Due to the restricted connectivity among these three regions, it is suggested to consider them as separate management areas in the design of MPA networks.

molecular biology↗

bioRxiv2021

Resolving the Dynamic Motions of SARS-CoV-2 nsp7 and nsp8 Proteins Using Structural Proteomics

Coronavirus (CoV) non-structural proteins (nsps) assemble to form the replication-transcription complex (RTC) responsible for viral RNA synthesis. nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase (RdRp) and other nsps. To date, no structure of full-length SARS-CoV-2 nsp7:nsp8 complex has been published. Current understanding of this complex is based on structures from truncated constructs or with missing electron densities and complexes from related CoV species with which SARS-CoV-2 nsp7 and nsp8 share upwards of 90% sequence identity. Despite available structures being solved using crystallography and cryo-EM representing detailed snapshots of the nsp7:nsp8 complex, it is evident that the complex has a high degree of structural plasticity. However, relatively little is known about the conformational dynamics of the complex and how it assembles to interact with other nsps. Here, the solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS), illuminate the structural dynamics of the SARS-CoV-2 full-length nsp7:nsp8 complex. The results presented from the two techniques are complementary and validate the interaction surfaces identified from the published three-dimensional heterotetrameric crystal structure of SARS-CoV-2 truncated nsp7:nsp8 complex. Furthermore, mapping of XL-MS data onto higher order complexes suggests that SARS-CoV-2 nsp7 and nsp8 do not assemble into a hexadecameric structure as implied by the SARS-CoV full-length nsp7:nsp8 crystal structure. Instead our results suggest that the nsp7:nsp8 heterotetramer can dissociate into a stable dimeric unit that might bind to nsp12 in the RTC without altering nsp7-nsp8 interactions.

biophysics↗

bioRxiv2020

SARS-CoV-2 targets cortical neurons of 3D human brain organoids and shows neurodegeneration-like effects

COVID-19 pandemic caused by SARS-CoV-2 infection is a public health emergency. COVID-19 typically exhibits respiratory illness. Unexpectedly, emerging clinical reports indicate that neurological symptoms continue to rise, suggesting detrimental effects of SARS-CoV-2 on the central nervous system (CNS). Here, we show that a Dusseldorf isolate of SARS-CoV-2 enters 3D human brain organoids within two days of exposure. Using COVID-19 convalescent serum, we identified that SARS-CoV-2 preferably targets soma of cortical neurons but not neural stem cells, the target cell type of ZIKA virus. Imaging cortical neurons of organoids reveal that SARS-CoV-2 exposure is associated with missorted Tau from axons to soma, hyperphosphorylation, and apparent neuronal death. Surprisingly, SARS-CoV-2 co-localizes specifically with Tau phosphorylated at Threonine-231 in the soma, indicative of early neurodegeneration-like effects. Our studies, therefore, provide initial insights into the impact of SARS-CoV-2 as a neurotropic virus and emphasize that brain organoids could model CNS pathologies of COVID-19. One sentence summaryCOVID-19 modeling in human brain organoids

cell biology↗

bioRxiv2019

Molecular and structural mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir

Hepatitis C virus (HCV), causative agent of chronic viral hepatitis, infects 71 million people worldwide and is divided into seven genotypes and multiple subtypes with sequence identities between 68 to 82%. While older generation direct-acting antivirals (DAAs) had varying effectiveness against different genotypes, the newest NS3/4A protease inhibitors including glecaprevir (GLE) have pan-genotypic activity. The structural basis for pan-genotypic inhibition and effects of polymorphisms on inhibitor potency were not well known due to lack of crystal structures of GLE-bound NS3/4A or genotypes other than 1. In this study, we determined the crystal structures of NS3/4A from genotypes 1a, 3a, 4a and 5a in complex with GLE. Comparison with the highly similar grazoprevir (GZR) indicated the mechanism of GLEs drastic improvement in potency. We found that while GLE is highly potent against wild type NS3/4A of all genotypes, specific resistance-associated substitutions (RASs) confer orders of magnitude loss in inhibition. Our crystal structures reveal molecular mechanisms behind pan-genotypic activity of GLE, including potency loss due to RASs at D168. Our structures permit for the first time analysis of changes due to polymorphisms among genotypes, providing insights into design principles that can aid future drug development and potentially can be extended to other proteins.

biochemistry↗