Biology subjects

Yu, X. A.

Publications and source records attributed to Yu, X. A..

4 recordsLinked to original sources

bioRxiv2025

Vividness of mental imagery is a broad trait measure of internally generated visual experiences

Research on mental visual imagery typically relies on vividness ratings. However, vividness is ill-defined as it lacks an objective reference. Here, we present survey results that suggest vividness is nevertheless a robust measure. It explains individual differences of a broad range of subjective experiences, from the detail of mental imagery, the propensity to report having other internally generated visual experiences, and the vividness of visual dreams. Critically, simple vividness ratings can replace the protracted questionnaires commonly used for this purpose and reduce methodological issues with these instruments. We further find that vividness is closely linked with the experience of "seeing" mental images or projecting them into the external world. People who report seeing mental images with their eyes shut are also more likely to experience externally projected imagery. Nevertheless, many people report having mental depictions but without seeing. Overall, our results indicate we should redefine visual aphantasia to distinguish individuals with faint or unseen visual images from those completely lacking a pictorial representation.

neuroscience↗

bioRxiv2024

Individual differences distinguish mechanisms underlying contextual size illusions

Previous research suggests the magnitudes of the Ebbinghaus, Delboeuf, Ponzo, and tilt illusions all depend on the cortical distance between the neural representations of target stimuli and the surrounding context. However, several psychophysical studies found no compelling association between these illusions, calling this hypothesis into question. Here we ask if these discrepant reports could arise from methodological differences between these studies. We ran a battery of visual size illusion and basic discrimination tasks with carefully matched geometric properties, using a classic forced-choice design. In our small, homogenous sample, the Ebbinghaus and Delboeuf illusion magnitudes were strongly correlated, consistent with the idea that they reflect the same underlying mechanism when other sources of individual differences are minimised. Ponzo illusion magnitude also correlated with these two illusions, although less strongly in the case of the Ebbinghaus. Interestingly, the classic arrowhead version of the Mueller-Lyer illusion did not correlate with any of the other illusions or even with the objective ability to discriminate line length. This suggests that an altogether separate process underlies this perceptual effect. We further demonstrate that presenting stimuli briefly with central fixation critically affects measurements of the Ebbinghaus illusion. Additionally, we found that measuring illusion magnitude via adjustment is less reliable compared to two-alternative forced-choice procedures. Taken together, our findings suggest that different tasks probe separable processes determining illusion measurements. They further highlight the importance of the experimental design when testing relationships between perceptual effects and their links to neural processing.

neuroscience↗

bioRxiv2024

Genome-wide sweeps create fundamental ecological units in the human gut microbiome

The human gut microbiome is shaped by diverse selective forces originating from the host and associated environmental factors, and in turn profoundly influences health and disease. While the association of microbial lineages with various conditions has been shown at different levels of phylogenetic differentiation, it remains poorly understood to what extent unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations. Here we show that a pervasive mechanism differentiating bacteria in the microbiome are genome-wide selective sweeps, leading to population structure akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others within its niche followed by re-diversification, and manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes, and we find that genome-wide sweeps originate under a wide regime of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest sweep clusters can spread globally within decades, and this process has occurred repeatedly throughout human history. We show, as an example, that the ecological differentiation of sweep clusters forms populations highly associated with age and colorectal cancer. Our analysis elucidates an evolutionary mechanism for the observation of stably inherited strains with differential associations and provides a theoretical foundation for analyzing adaptation among co-occurring microbial populations.

microbiology↗

bioRxiv2023

Magnetogenetic cell activation using endogenous ferritin

The ability to precisely control the activity of defined cell populations enables studies of their physiological roles and may provide therapeutic applications. While prior studies have shown that magnetic activation of ferritin-tagged ion channels allows cell-specific modulation of cellular activity, the large size of the constructs made the use of adeno-associated virus, AAV, the vector of choice for gene therapy, impractical. In addition, simple means for generating magnetic fields of sufficient strength have been lacking. Toward these ends, we first generated a novel anti-ferritin nanobody that when fused to transient receptor potential cation channel subfamily V member 1, TRPV1, enables direct binding of the channel to endogenous ferritin in mouse and human cells. This smaller construct can be delivered in a single AAV and we validated that it robustly enables magnetically induced cell activation in vitro. In parallel, we developed a simple benchtop electromagnet capable of gating the nanobody-tagged channel in vivo. Finally, we showed that delivering these new constructs by AAV to pancreatic beta cells in combination with the benchtop magnetic field delivery stimulates glucose-stimulated insulin release to improve glucose tolerance in mice in vivo. Together, the novel anti-ferritin nanobody, nanobody-TRPV1 construct and new hardware advance the utility of magnetogenetics in animals and potentially humans.

bioengineering↗