Biology subjects

Gabdulkhakov, A.

Publications and source records attributed to Gabdulkhakov, A..

3 recordsLinked to original sources

bioRxiv2026

Distinct and overlapping correlates of fear acquisition and extinction across different neuroimaging modalities

Interindividual differences in fear acquisition and extinction have been related to variation in specific brain correlates. However, variability in experimental setups complicates the integration of findings. Here, we present a combined fear acquisition (n = 101) and extinction (n = 88) study from which we obtained distinct microstructural, macrostructural, and connectivity brain properties with magnetic resonance imaging in healthy, young participants. The properties included regional brain volume, cortical surface area and thickness, neurite density and orientation dispersion, and nodal efficiency of structural and functional connectivity. Fear responses were quantified as changes in skin conductance. Data from 360 cortical and 16 subcortical brain regions as well as the efficiency of network connections between them were used as independent variables in bootstrapped and cross-validated regularized regression models. Results show that numerous brain regions, spanning the so-called 'fear and extinction network' and extending beyond it, contribute to fear acquisition, to extinction, or dynamically shift between both phases. For several brain regions, data from multiple imaging modalities showed a high degree of concordance for several brain regions. These findings call for further research to examine the potential interplay between brain correlates shaping fear acquisition and extinction, as opposed to studying the imaging modalities in isolation.

neuroscience↗

bioRxiv2026

BOLD signals of learning dynamics across and within trials beyond the classical fear and extinction network

Human functional magnetic resonance imaging studies of fear conditioning often average neural responses across trials, potentially obscuring transient activations that vary across learning. In this study with 139 participants, we examined finer temporal dynamics of conditioned responding by analyzing three 2s segments within the conditioned stimulus (CS) presentation period across each quarter of fear acquisition and extinction training. This approach revealed distinct, time-specific engagement of regions within fear- and safety-related networks, both within and across trials. In particular, different activation patterns emerged across the three trial segments during CS presentation, indicating that neural responses were not limited to CS onset. We observed a more classical activation pattern at 0s relative to CS onset that diverged in later trial segments, most notably involving the amygdala, hippocampus, and prefrontal cortex (PFC) structures such as vmPFC present exclusively in 2s and 4s trial segments. We also found sustained activations consistent across all blocks of trials, such as right vlPFC activation 4s after CS onset across all fear acquisition quarters. These findings suggest that conditioned fear and safety processing unfold as dynamic spatiotemporal cascades and highlight the importance of modeling later responses following CS onset rather than focusing exclusively on onset-related activation.

neuroscience↗

bioRxiv2025

Determination of the water network surrounding the type I pilus from E. coli by cryo-electron microscopy

Type 1 pili are protein filamentous surface structures of Gram-negative bacteria that mediate adhesion to host and play a crucial role in infection. Here, we report the cryogenic electron microscopy structure of the type 1 pilus from E. coli K-12 comprising 15 subunits of the major protein pilin FimA. The final resolution of EM reconstruction was estimated to be in the range from 2.09 to 2.30 [A], which is higher than that of the previously published structure. This improvement in the resolution enabled us to refine side-chain conformations to reliably determine the distances between the side-chain residues participating in the intersubunit interactions, and determine a network of water molecules surrounding the pilus rod. The analysis revealed that water contributes to intersubunit stabilization both through discrete bridging interactions and through extended hydrogen-bonded clusters, thereby supporting both the rigidity and flexibility of the filament. Comparison with a homologous high-resolution pilus model from enterotoxigenic E. coli showed that nearly all "conserved" water molecules i.e., those that are present at equivalent positions in different subunits of our model occupy also equivalent positions across the two structures, under-scoring their functional relevance. At the same time, sequence-specific differences in hydration patterns were observed. These findings highlight the structural and functional importance of water in pilus architecture and provide a more detailed molecular framework for understanding bacterial adhesion. SynopsisThe improvement in the resolution of the Cryo-EM reconstruction for type I pilus from E. coli made it possible to determine the positions of water molecules surrounding the pilus rod and reveal a more detailed picture of interactions between different subunits of the rod.

molecular biology↗