Biology subjects

Qi, A.

Publications and source records attributed to Qi, A..

4 recordsLinked to original sources

bioRxiv2022

Genome-wide investigation of multiplexed CRISPR-Cas12a-mediated editing in rice

We previously reported highly specific genome editing in rice by CRISPR-Cas9 and Cas12a with single DNA double strand break (DSB) (Tang et al., 2018). Two concurrent DSBs by CRISPR-Cas9 could generate defined deletions (Zhou et al., 2014), inversions (Schmidt et al., 2020), and translocations (Beying et al., 2020). Off-target effects of many simultaneous DSBs are unknown in plants. Here, we used whole-genome sequencing (WGS) to investigate off-target effects in rice plants edited by highly multiplexable CRISPR-Cas12a systems (Zhang et al., 2021). Our WGS study revealed highly specific multiplexed genome editing by CRISPR-Cas12a. We found low-frequency large chromosomal deletion and duplication events in plants that endured many (e.g., >50) simultaneous DSBs, but not in plants that endured a lower order DSBs (e.g., <10). While our short reads sequencing may not capture all chromosomal rearrangements, our results nevertheless shed important light on the analysis and regulation of engineered crops derived from multiplexed genome editing.

genomics↗

bioRxiv2022

Larger cerebral cortex is genetically correlated with greater frontal area and dorsal thickness

Human cortical expansion has occurred non-uniformly across the brain. We assessed the genetic architecture of cortical global expansion and regionalization by comparing two sets of genome-wide association studies of 24 cortical regions with and without adjustment for global measures (i.e. total surface area, mean cortical thickness) using a genetically-informed parcellation in 32,488 adults. We found 393 and 756 significant loci with and without adjusting for globals, respectively, among which 8% and 45% loci were associated with more than one region. Results from analyses without adjustment for globals recounted loci associated with global measures. Genetic factors that contribute to total surface area of the cortex particularly expand anterior/frontal regions, whereas those contributing to thicker cortex predominantly increase dorsal/frontal-parietal thickness. Interactome-based analyses revealed significant overlap of global and regional genetic modules, enriched for neurodevelopmental and immune system pathways. Consideration of global measures is important in understanding the genetic variants underlying cortical morphology.

neuroscience↗

bioRxiv2022

Efficient learning in children with rapid GABA boosting after training

It is unclear why and how children learn more efficiently than adults, although inhibitory systems, which play an important role in stabilizing learning, are immature in children. Here, we found that despite a lower baseline concentration of {gamma}-aminobutyric acid (GABA) in early visual cortical areas in children (8 to 11 years old) than adults (18 to 35 years old), children exhibited a rapid boost of GABA immediately after visual training, whereas the concentration of GABA in adults remained unchanged after training. Moreover, behavioral experiments showed that children stabilized visual learning much faster than adults, showing rapid development of resilience to retrograde interference. These results together suggest that inhibitory systems in childrens brains are more dynamic and adapt more quickly to stabilize learning than in adults. One Sentence SummaryChildren learn more efficiently than adults due to faster stabilization of learning with rapid GABA boosting after training.

neuroscience↗

bioRxiv2019

Perceptual learning of lesions in mammograms induced by response feedback during training

Detecting subtle lesions in mammograms indicative of early breast cancer usually requires years of experience. Well-designed training paradigms could be a strong tool for promoting perceptual learning (PL) with rapid and long-lasting improvement in detectability of these subtle mammographic lesions. Given that PL occurs without feedback about the accuracy of subjects responses, the role of feedback has been completely ignored in clinical applications of PL. However, in this study, we found that the contents of the feedback profoundly and differentially influence the formation and retention of PL to detect calcification and architectural distortion lesions, two types of mammographic lesions that are frequently missed in mammographic screenings. We trained subjects to detect one type of lesion in a mammogram and manipulated the content of the response feedback during training for 3 groups (no feedback, correctness only, and both correctness and location of the lesion). We found that PL occurred for both lesions when both correctness and location feedback were provided. PL also occurred for calcifications but not for distortions when only correctness was provided. No learning occurred without feedback for either lesion. A retest conducted six months later showed that PL was retained only in the group with both correctness and location feedback for both types of lesions. In contrast to the general consensus of basic PL studies, our results demonstrate that the content of the response feedback is a determining factor in forming and retaining PL to detect mammographic lesions.

neuroscience↗