Biology subjects

Pu, Y.

Publications and source records attributed to Pu, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Inflammatory suppression and cancer-associated bypass of the b0,+selenium-utilization program in the human intestine

The b0,+ transporter (SLC3A1/SLC7A9) imports cystine and selenocystine at the enterocyte apical membrane and defines a selenium-utilization program in the healthy human intestine (He et al., bioRxiv 2026); how this program is altered in disease is unknown. Using a multi-cohort single-cell framework with donor-level statistics, we find that inflammation and cancer remodel a single epithelial redox-currency axis in opposite directions. In adult Crohns disease, b0,+ co-expression in small-intestinal enterocytes was suppressed (median 4.9% vs 34% positive; P = 0.008) but preserved in paediatric IBD; this loss reflected replacement of b0,+-high mature enterocytes by a dedifferentiated state rather than transcriptional disruption, with the SLC7A9-SELENOP coupling intact. Downstream, GPX4 alone was selectively suppressed while the selenocysteine-incorporation machinery was preserved, priming the epithelium for ferroptosis in a severity-graded manner. Inflammatory cytokines (IFN{gamma}, TNF) suppressed the selenium pole in small-intestinal enteroids, and a network knockout indicated that b0,+ supports the selenoproteome through substrate supply rather than transcriptional control; an independent patient proteome and a Caco-2 polarization model corroborated the axis. Colorectal-cancer colonocytes showed the opposing pole, near-absent b0,+ with induction of the xCT/thiol program (P = 5.6 x 10-5) and a ferroptosis-resistant configuration. Thus b0,+ marks the supply node of a dual-pole selenium-thiol axis: inflammation collapses the selenium pole toward a ferroptosis-prone dedifferentiated state, whereas cancer bypasses it toward an xCT antioxidant pole. The baseline axis state is an exploratory correlate of anti-TNF response and a candidate point of disease-associated vulnerability.

molecular biology↗

bioRxiv2026

Dormant Bacteria's Fatal Attraction to RNA Bacteriophages

Phages are the most abundant biological entities on Earth, yet RNA phages are strikingly scarce compared to their DNA counterparts--a long-standing mystery in phage biology. Here, we use dsRNA phage phiYY as a model to demonstrate that while RNA phages efficiently infect growing bacteria, they are gradually eliminated inside dormant bacteria through weak and time-dependent ROS-mediated damage. The RNA phages decline over days rather than through immediate clearance inside dormant bacteria. Accordingly, scavenging ROS with mannitol or overexpressing ROS degradation enzymes AhpB/TrxB2 rescues RNA phages from elimination. Crucially, because the underlying ROS-mediated RNA damage is minimal, RNA phage survival hinges on genomic redundancy. In single-phage infections, the lone RNA genome is highly vulnerable to cumulative damage and is eventually inactivated. In contrast, during co-infection by multiple RNA phages, the presence of multiple genome copies provides functional redundancy, thereby allowing a fraction of RNA phages to survive inside dormant bacteria. Given that most environmental bacteria are dormant and subject to heterogeneous phage infection, this copy number-dependent vulnerability offers a possible explanation for the scarcity, but not perish, of RNA phages in nature.

microbiology↗

bioRxiv2026

On-target toxicity of GSPT1 molecular glue degraders in mice

Thalidomide is teratogenic in humans but not in rodents due to species-specific differences in the sequence of Cereblon (CRBN), an E3 ubiquitin ligase targeted by thalidomide and its derivative molecular glue degraders (MGDs). This species divergence has hindered the accurate prediction of MGD-induced toxicities in standard laboratory animals. GSPT1 MGDs, such as CC-90009, have shown potent anticancer activities in preclinical models and leukemia patients; however, their clinical development was challenging due to severe adverse effects. This highlights the critical need to characterize on-target toxicities in relevant animal models to exploit the therapeutic safety of this class of MGDs. Here, we generated humanized CrbnV380E and CrbnV380E/I391V knock-in mouse strains, in combination with a degradation-resistant Gspt1G574N strain, to interrogate the in vivo on-target effects of CC-90009 and its analog CC-885. We found that targeted GSPT1 depletion in mice led to rapid mortality, preceded by multiple dysfunctions including intestinal obstruction, liver damage, splenic atrophy, and hematological abnormalities. Remarkably, these toxicities, along with the underlying transcriptional perturbations, were completely rescued by the undegradable Gspt1G574N mutant, establishing a definitive causal link between GSPT1 degradation and systemic injury. Induced proximity and degradation proteomic analyses revealed that GSPT1 loss triggered a secondary downregulation of many proteins, including MYC, PLK1 and CDK4, which were not directly recruited by these MGDs to CRBN. Collectively, our data define the in vivo on-target toxicities associated with endogenous GSPT1 degradation and provide a genetic framework to guide the preclinical safety evaluation of CRBN-based MGD therapeutics.

molecular biology↗

bioRxiv2026

Mechanism study on lactic acid promoting intervertebral disc degeneration by regulating senescence and DNA damage of cartilage endplate stem cells

Intervertebral disc degeneration, a leading cause of low back pain with incompletely elucidated molecular mechanisms, was studied via integrated in vivo/vitro approaches. This study first reveals that lactic acid accelerates intervertebral disc degeneration by inducing cartilage endplate stem cells senescence and DNA damage, thereby activating the P16/P21/P53-centered senescence pathway. In a rat tail vertebra puncture-induced intervertebral disc degeneration model, degenerated discs exhibited increased lactic acid levels, narrowed intervertebral spaces, and disrupted nucleus pulposus structure (P<0.05). In vitro, 0/2/6/10 mM lactic acid dose-dependently suppressed cartilage endplate stem cells viability (10 mM group: 15.7% of the control), elevated intracellular reactive oxygen species (ROS, 2.8-fold relative to the control), induced G0 cell cycle arrest (10 mM group: 85.63%), reduced EdU-positive cells (8.62%), and increased {beta}-galactosidase-positive cells (10 mM group: 33.06%) and {gamma}-H2AX foci (all P<0.01).Molecularly, lactic acid significantly upregulated P16 (2.1-fold), P21 (3.1-fold), P53 (2.4-fold), and {gamma}-H2AX (1.8-fold). In vivo intervertebral disc injection confirmed a positive correlation between lactic acid concentration and intervertebral disc degeneration severity. This study clarifies lactic acids role in intervertebral disc degeneration via the "oxidative stress-cell cycle arrest-cellular senescence" axis, advancing understanding of intervertebral disc degeneration pathogenesis and providing a basis for targeted therapies against lactic acid metabolism.

cell biology↗

bioRxiv2025

Ethylene Glycol Monomethyl Ether Altered Rat Sperm Small RNAs with Critical Developmental Roles

Abstract/SummaryEthylene glycol monomethyl ether (EGME) is a testicular germ cell toxicant that selectively targets spermatocytes. In rats, male-only EGME exposure reduces mating success and can lead to an increase in resorbed fetuses. In a previous study, five-day exposure to 50, 60, or 75 mg/kg/d EGME in male rats led to a decrease in sperm motility and increase in retained spermatid heads with a lowest observed adverse effect level (LOAEL) of 75 mg/kg/d. At 60 mg/kg/d, EGME exposure altered the proportion of sperm small RNA reads mapped to different small RNA categories and the distribution of read lengths. To understand the possible role of sperm sncRNAs in EGME-mediated reduction in spermatogenesis, fertility, and embryonic development, we analyzed sperm sncRNA data from EGME-treated male rats to identify differential expression at the individual RNA level. EGME treatment resulted in dose-dependent increases in the expression levels of microRNAs (miRNAs), piRNAs, and tRNA-derived small RNAs (tsRNAs), and mixture of dose-dependent increases and decreases in abundance of rsRNA reads. We identified 12 miRNAs that were differentially expressed at all EGME doses, with a monotonic, dose-dependent increase. High-confidence targets of these 12 miRNAs are known to be expressed in pre-implantation embryos and statistically enriched for Gene Ontology (GO) biological processes related to early development, such as cell fate commitment and regulation of developmental growth. These results demonstrated that the EGME-induced changes in sperm sncRNA levels were reproducible, dose-dependent, and provided a putative mechanism of paternal EGME effects on embryonic development, which will be investigated in future studies.

pharmacology and toxicology↗

bioRxiv2025

Native-state dimerization drives misfolding and aggregation of Cys-depleted variants of cataract-associated human lens γD-crystallin

Cataract, the leading cause of blindness worldwide, results from age-related misfolding and aggregation of long-lived crystallin proteins in the eye lens. The cytoplasm of fiber cells in the lens core becomes increasingly oxidizing with age, allowing non-native disulfides to drive light-scattering aggregation of {gamma}-crystallins. Despite this vulnerability to non-native disulfides, and despite lacking any native-state disulfides, {gamma}-crystallins are unexpectedly Cys-rich. To understand this paradox, we investigated how replacing all four Cys residues in the aggregation-prone N-terminal domain of {gamma}D-crystallin affects its stability and aggregation. Cys removal precludes the disulfide-driven aggregation pathway we reported previously. Here, we characterize two full-length human {gamma}D-crystallin variants: C18S/C32S/C41S/C78S ("NCS") and C18T/C32A/C41A/C78A ("NCA/T"). Thermodynamic and kinetic stability measurements indicate the N-terminal domain was greatly destabilized in both variants relative to WT, with NCS more destabilized than NCA/T. Upon mild heating or partial denaturation, both variants formed light-scattering aggregates, which were amorphous by transmission electron microscopy. Surprisingly, the aggregation proceeded exclusively from a dimer of natively folded molecules held together by a C-terminal disulfide bridge. These dimers form readily even in the WT protein, and evidence of them has been found in the lens. Aggregation was strongly suppressed by the lenss native chemical chaperone, myo-inositol. The aggregation rate depended linearly on protein concentration, indicating that the rate limiting step was a transformation of the natively-folded to misfolded molecules within the dimer. We propose that many age-related chemical modifications could destabilize the native fold of human {gamma}D-crystallin, favor misfolding within disulfide-bridged dimers, and thereby cause aggregation.

biochemistry↗

bioRxiv2025

Repurposing base editors for targeted knock-in and simultaneous knockouts to generate multiplex-edited allogeneic CAR T cells with minimal translocations

The CRISPR-Cas system enables precise genome engineering of cell therapies. For allogeneic applications, multiplex editing is frequently required to improve efficacy, persistence, and safety. However, strategies involving multiple DNA double-strand breaks (DSBs) induce genotoxicity by provoking chromosomal aberrations. Base editors, which enable sequence changes without generating DSBs, are widely used for gene disruption, but their capacity for gene insertion remains unexplored. Here, we developed Base editor-mediated knock-in (BEKI), a non-viral platform that allows targeted transgene insertion in parallel with multiplex gene disruption using a single base editor. Repurposing the Cas9 nickase domain of base editors generates paired nicks, inducing homology-directed repair (HDR). In human T cells, optimized guide RNA orientation and nick distance, together with HDR-enhancing modulators, enabled efficient transgene knock-in at the TRAC, CD3{zeta}, B2M, and CD3{varepsilon} loci. Simultaneous base editing of multiple additional genes produced chimeric antigen receptor (CAR) T cells with increased cytokine secretion, drug resistance, and resistance to allo-rejection. Compared to multiplex editing with Cas9, BEKI markedly reduced chromosomal translocations. BEKI therefore provides a streamlined, scalable strategy for multiplex CAR T-cell engineering with a single enzyme, offering a safer route to clinical-grade manufacturing of off-the-shelf therapies for cancer and autoimmune diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/676172v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@f5f6e5org.highwire.dtl.DTLVardef@246411org.highwire.dtl.DTLVardef@125a478org.highwire.dtl.DTLVardef@510278_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Versatile and efficient non-viral integration of large transgenes in human T cells via CRISPR knock-in and engineered integrases

Current gene transfer methods often lack the precision, versatility, or efficiency when integrating large transgenes, limiting the ability to engineer therapeutic T-cells with more complex payloads. Here, we report one-pot PASTA (Programmable and Site-specific Transgene Addition), a non-viral genome engineering strategy for large gene insertion that combines CRISPR-Cas-mediated homology-directed repair (HDR) and site-specific recombination via serine integrases. Using one-pot PASTA with the Bxb1 integrase, we demonstrate efficient integration of transgenes at multiple genomic loci relevant for T-cell engineering (e.g., TRAC, B2M, CD3E, CD3Z, GAPDH). For constructs > 8 kb, one-pot PASTA outperforms conventional HDR by 19-fold on average and prime-editing-assisted site-specific integrase gene editing (PASSIGE) by 5-fold. This enables the delivery of multi-cistronic cargo to generate dual-antigen targeting CAR T-cells with a safety-switch that overcome antigen escape in lymphoma models. Finally, one-pot PASTA can be further optimized with improved integrase enzymes, such as engineered variants of Pa01 or Bxb1, and plasmids with minimized backbones. In summary, one-pot PASTA represents a versatile and scalable platform for precise, non-viral gene insertion in T-cells.

synthetic biology↗

bioRxiv2025

Legacy of the lost and pressure of the present: Malagasy plant seeds retain megafauna dispersal signatures but downsize under human footprint

Past megafaunal extinctions and ongoing declines of remaining large-bodied frugivores limit the dispersal of large-seeded plants, contributing to their (local) demise, thereby downsizing plant seeds across assemblages. Here, we test this hypothesis by integrating trait and distribution data for 2,852 endozoochorous plant species, 48 extant and 15 extinct frugivore species across 361 assemblages on Madagascar. Using structural equation models, we show that mega-seeded plants - with seeds that are too large to be swallowed by any extant Malagasy frugivore - have larger seeds in assemblages where past megafrugivores were larger, highlighting the legacy of past interactions on persisting mega-seeded plants. Furthermore, human footprint reduces seed sizes directly and indirectly by downsizing of extant frugivore in the assemblages. Such human-driven seed downsizing can lead to erosions of important ecosystem functions such as tropical forest carbon storage.

ecology↗

bioRxiv2025

Revisiting the need for mRNA nucleoside modification in CAR T cell engineering

mRNA-based chimeric antigen receptor (CAR)-T cells offer the promise of enhanced safety and simplified manufacturing. However, in vitro-transcribed (IVT) mRNA is known to trigger antiviral immune responses, inflammatory signaling, and apoptosis in transfected cells. To address these challenges and enable efficient IVT-mRNA expression, modified nucleosides, such as N1-methyl-pseudouridine (m1{Psi}), have become the gold standard for CAR-T cell production, albeit at increased cost. In this study, immune responses to IVT-mRNA were evaluated across five primary human cell types, including T-cells. Unexpectedly, T-cells, unlike other immune and non-immune cell types tested, exhibited no immune activation in response to unmodified mRNA. T-cell viability and cytokine secretion patterns remained unaffected, regardless of whether unmodified mRNA was delivered via lipid nanoparticles (LNPs) or electroporation. Furthermore, CAR expression levels in T-cells were not influenced by mRNA modification with m1{Psi} or 5-methoxy-uridine (5moU) nucleosides. The absence of nucleoside modifications did not compromise CAR-T cell cytotoxic potency, demonstrating that such modifications are not required for producing functional CAR-T cells. These findings eliminate the need for nucleoside modification in T-cell mRNA, simplifying and reducing the cost of CAR-T cell manufacturing while positioning IVT-mRNA as a highly efficient and minimally invasive tool for CAR-T cell engineering.

bioengineering↗

bioRxiv2024

DeepAssembly2: A Web Server for Protein Complex Structure Assembly Based on Domain-Domain Interactions

Proteins often perform biological functions by forming complexes, thereby accurately predicting the structure of protein complexes is crucial to understanding and mastering their functions, as well as facilitating drug discovery. Protein monomeric structure prediction has made a breakthrough in recent years, but the accurate prediction of complex structure remains a challenge. In this work, we present DeepAssembly2, a web server for automatically assembling protein complex structure based on domain-domain interactions. First, the features are constructed according to the input complex sequence and monomeric structures, then these features are used to predict the inter-chain residue distance through a deep learning model, and finally, the complex structure is assembled under the guidance of inter-chain residue distances. Compared with the previously developed version, DeepAssembly2 is trained on a newly constructed inter-chain domain-domain interaction dataset. Meanwhile, several important features have been added, such as Interface Residue Propensity and Ultrafast Shape Recognition. In addition, we introduced the inter-chain residue distance from the AlphaFold-Multimer model to further improve the accuracy. Finally, we also integrate our recently developed model quality assessment method to select the output models. The performance of DeepAssembly2 is significantly improved compared with the previous version, providing a solution for large protein complex structure modeling through divide-and-conquer assembly strategy, and is expected to provide new insights and an effective tool for drug development, vaccine design, etc. The web server of DeepAssembly2 is freely available at http://zhanglab-bioinf.com/DeepAssembly/.

bioinformatics↗

bioRxiv2024

Global brain asymmetry and its variations in aging and related diseases

Functional lateralization is a cardinal feature of human brain, and deviations from typical lateralization are observed in various brain disorders. Although this phenomenon has been widely acknowledged in the field of human neuroscience, decades of research have shown that it is a challenge to bridge the gap between (a)typically lateralized functions and hemispheric differences in structure (termed structural asymmetry). To address this important question, the present study employed the state-of-the-art machine learning techniques to investigate the brain structural asymmetry and its associations with cognitive functions, aging, and aging-related diseases, by integrating large-scale datasets. Our proposed multivariate approach revealed previously unknown and substantial structural differences between the left and right hemispheres, and established the associations between the global brain asymmetry and lateralized functions including hand motor and emotion processing. Furthermore, at the population level we mapped the aging trajectories of the global brain asymmetry, and unveiled significant diagnosis-specific variations in patients with Alzheimers disease and Parkinsons disease, and individuals carrying a relevant genetic risk for atypical brain aging (i.e., APOE4 carriers). These results demonstrated left-hemisphere-linked changes in aging, which has challenged the traditional "right hemi-aging" model, and offered a promising approach for assessing brain aging and related diseases. Overall, our study with a novel approach presents one of the largest-scale investigation of global brain asymmetry, and takes an important step forward in understanding the intricate interplay between structural asymmetry, lateralized functions, and brain aging in health and disease. Significance statementFunctional lateralization is fundamental to the human brain, with deviations linked to various brain disorders. Bridging the gap between functional lateralization and structural asymmetry has been a long-standing challenge. Using advanced machine learning and large-scale datasets, this study introduced a multivariate global brain asymmetry approach and revealed previously unidentified structural differences between the brain hemispheres, correlating these with cognitive functions, aging, and diseases like Alzheimers and Parkinsons. Contrary to the traditional "right hemi-aging" model, we found left-hemisphere-linked aging changes. This work provides new insights into brain asymmetry, lateralized functions, and aging, offering a promising approach for assessing brain health and disease. Classifications: Biological Sciences (Psychological and Cognitive Sciences);

neuroscience↗

bioRxiv2024

Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication

Defining the subset of cellular factors governing SARS-CoV-2 replication can provide critical insights into viral pathogenesis and identify targets for host-directed antiviral therapies. While a number of genetic screens have previously reported SARS-CoV-2 host dependency factors, these approaches relied on utilizing pooled genome-scale CRISPR libraries, which are biased towards the discovery of host proteins impacting early stages of viral replication. To identify host factors involved throughout the SARS-CoV-2 infectious cycle, we conducted an arrayed genome-scale siRNA screen. Resulting data were integrated with published datasets to reveal pathways supported by orthogonal datasets, including transcriptional regulation, epigenetic modifications, and MAPK signalling. The identified proviral host factors were mapped into the SARS-CoV-2 infectious cycle, including 27 proteins that were determined to impact assembly and release. Additionally, a subset of proteins were tested across other coronaviruses revealing 17 potential pan-coronavirus targets. Further studies illuminated a role for the heparan sulfate proteoglycan perlecan in SARS-CoV-2 viral entry, and found that inhibition of the non-canonical NF-kB pathway through targeting of BIRC2 restricts SARS-CoV-2 replication both in vitro and in vivo. These studies provide critical insight into the landscape of virus-host interactions driving SARS-CoV-2 replication as well as valuable targets for host-directed antivirals.

systems biology↗

bioRxiv2024

Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma.

Cancer cells show remarkable plasticity and can switch lineages in response to the tumor microenvironment. Cellular plasticity drives invasiveness and metastasis and helps cancer cells to evade therapy by developing resistance to radiation and cytotoxic chemotherapy. Increased understanding of cell fate determination through epigenetic reprogramming is critical to discover how cancer cells achieve transcriptomic and phenotypic plasticity. Glioblastoma is a perfect example of cancer evolution where cells retain an inherent level of plasticity through activation or maintenance of progenitor developmental programs. However, the principles governing epigenetic drivers of cellular plasticity in glioblastoma remain poorly understood. Here, using machine learning (ML) we employ cross-patient prediction of transcript expression using a combination of epigenetic features (ATAC-seq, CTCF ChIP-seq, RNAPII ChIP-seq, H3K27Ac ChIP-seq, and RNA-seq) of glioblastoma stem cells (GSCs). We investigate different ML and deep learning (DL) models for this task and build our final pipeline using XGBoost. The model trained on one patient generalizes to another one suggesting that the epigenetic signals governing gene transcription are consistent across patients even if GSCs can be very different. We demonstrate that H3K27Ac is the epigenetic feature providing the most significant contribution to cross-patient prediction of gene expression. In addition, using H3K27Ac signals from patients-derived GSCs, we can predict gene expression of human neural crest stem cells suggesting a shared developmental epigenetic trajectory between subpopulations of these malignant and benign stem cells. Our cross-patient ML/DL models determine weighted patterns of influence of epigenetic marks on gene expression across patients with glioblastoma and between GSCs and neural crest stem cells. We propose that broader application of this analysis could reshape our view of glioblastoma tumor evolution and inform the design of new epigenetic targeting therapies.

cancer biology↗

bioRxiv2024

Cyclic di-GMP as an Antitoxin Regulates Bacterial Genome Stability and Antibiotic Persistence in Biofilms

Biofilms are complex bacterial communities characterized by a high persister prevalence, which contributes to chronic and relapsing infections. Historically, persister formation in biofilms has been linked to constraints imposed by their dense structures. However, we observed an elevated persister frequency accompanying the stage of cell adhesion, marking the onset of biofilm development. Subsequent mechanistic studies uncovered a comparable type of toxin-antitoxin (TA) module (TA-like system) triggered by cell adhesion, which is responsible for this elevation. In this module, the toxin HipH acts as a genotoxic deoxyribonuclease, inducing DNA double strand breaks and genome instability. While the second messenger c-di-GMP functions as the antitoxin, exerting control over HipH expression and activity. The dynamic interplay between c-di-GMP and HipH levels emerges as a crucial determinant governing genome stability and persister generation within biofilms. These findings unveil a unique TA system, where small molecules act as the antitoxin, outlining a biofilm-specific molecular mechanism influencing genome stability and antibiotic persistence, with potential implications for treating biofilm infections.

microbiology↗

bioRxiv2024

Bacterial stress granule protects mRNA through ribonucleases exclusion

Membraneless droplets formed through liquid-liquid phase separation of ribonucleoprotein particles contribute to mRNA storage in eukaryotic cells. How such aggresomes contribute to mRNA dynamics under stress, and their functional role, is less understood in bacteria. Here we used multiple approaches including live-cell imaging, polymer physics modelling and transcriptomics to show that prolonged stress leading to ATP depletion in Escherichia coli results in increased aggresome formation, compaction, and selective mRNA enrichment within these aggresomes. Longer transcripts accumulate more in aggresomes than in the cytosol. Mass spectrometry and mutagenesis studies showed that mRNA ribonucleases are excluded from aggresomes due to electrostatic repulsion arising from their negative surface charges. Experiments with fluorescent reporters and disruption of aggresome formation showed that mRNA storage within aggresomes promoted rapid translation reactivation and associated with reduced lag phases during growth after stress removal. Our findings suggest that mRNA storage within aggresomes confers an advantage for bacterial survival and recovery from stress.

biophysics↗

bioRxiv2024

Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

In wheat (Triticum aestivum L.), yield component traits (YCTs) are the most important yield traits. Only several genes for YCTs have been originally cloned. The efficient cloning of genes for YCTs directly from wheat remains a challenge. Here, we proposed a strategy for cloning genes from quantitative trait loci (QTLs) by sequencing of recombinant inbred lines (RILs) (QTL-Seq-RIL). Using the TN18 x LM6 RIL population as an example, we identified 138 candidate unigenes (CUGs) for YCTs from 77 stable QTLs. The average of CUGs per QTL was 1.8, which enabled us to confirm the CUGs directly. We have confirmed seven CUGs, TaIFABPL, TaDdRp, TaRLK, TaTD, TaTFC3, TaKMT and TaSPL17, via the CRISPR/Cas9 system. Of these, six genes were found firstly to regulate YCTs in crops except for TaSPL17. Five CUGs (include TaSPL17) for which orthologous genes have been cloned previously with the same or similar agronomic functions. It is to say, 11 CUGs were preliminarily validated using a single RIL population. QTL-Seq-RIL provides an efficient method for rapid gene cloning using existing RIL populations.

plant biology↗

bioRxiv2024

Emotional prosody modulates visual mental imagery

Perceptual stimulis emotional properties are vital for human evolution and adaptation. While visual imagery is predominantly regarded as a weak form of perception, the influence of cross-modal emotional features on imagery is still unknown. The present study aims to investigate how emotional prosody modulates imagery quality (i.e., accuracy and clarity) and neural mechanisms using a combination of behavioral tasks and functional magnetic resonance imaging (fMRI). At the behavioral level, our results showed that frustrated conditions induced significant prosody effects on visual mental imagery quality measures, and the effects were particularly pronounced in individuals with lower imagery use tendency. At the neural level, compared with the neutral condition, the emotional prosody conditions (both happy and frustrated) showed stronger activation in various regions including the middle occipital gyrus, supporting the critical role of primary visual system in imagery. Moreover, compared to the frustrated prosody condition, the happy prosody showed stronger activation in the precuneus and anterior cingulate cortex, which are core components of the default mode network. A machine learning prediction analysis with a random forest model identified a significant brain-behavioral correlation between prosody-linked neural activity and individual imagery use tendency. A subsequent Shapley Additive exPlanations (SHAP) analysis further highlighted the primary visual and default mode regions as top contributors to this prediction. Taken together, these results provide new insights for the understanding of how emotional prosody modulates visual mental imagery, considering individual differences, and provide compelling evidence for incorporating emotion as important shaping factor in more general model for imagery.

neuroscience↗