Biology subjects

Ouyang, B.

Publications and source records attributed to Ouyang, B..

7 recordsLinked to original sources

bioRxiv2026

Resolving Gene-Metabolism Links through Multi-Metabolite mQTL Commonality Analysis

High-throughput metabolomics detects so many compounds that most studies use only a fraction of them, focusing on the few metabolites with an annotated structure or substructure. Metabolite genome-wide association studies of specialized metabolism detect many metabolite quantitative trait loci (mQTLs), but most associated metabolite features remain unannotated, limiting gene discovery. In leaves of 362 tomato accessions under control and water-deficit conditions, only 13 of the 826 metabolite features associated with 77 reproducible mQTLs were annotated with good confidence. To study the mQTLs with the largest impact, we developed commonality analysis, an approach that does not depend on well-studied pathways. Commonality analysis uses biologically defined groups, such as the features associated with one mQTL, to infer relatedness between metabolites. By identifying the fragments, neutral losses or mass transformations that are common in a group, it links the group to a substructure, pathway or reaction, and can extend annotation within the group. Most high-impact mQTLs had a significantly distinct fragment commonality, whose outstanding fragments suggested the pathway involved and its candidate gene. We demonstrate the approach in three representative mQTLs: (i) common fragments pointed to a sinapoyl-hexose pathway and a serine carboxypeptidase-like candidate acyltransferase; (ii) common fragments marked the features associated with a purine permease as nitrogen-containing, which isotope labeling then supported; (iii) a common 2.02 Da transformation pointed to a double-bond reduction and a putative reductase. Overexpression of each gene reproduced the commonality patterns, supporting the candidate genes and showing that the approach also applies to experimentally defined metabolite groups.

plant biology↗

bioRxiv2026

Maximum entropy model reveals frequent brain state switching in psychotic disorders in a multiversal brain function analysis

To design network-based treatments, it is critical to understand dynamic changes in brain networks over time. We comprehensively examined network structure using regional activation-only, pairwise-coactivation-only, and systems-level maximum entropy models (MEM) applied to the Human Connectome Project-Early Psychosis (HCP-EP) resting fMRI data (patients=109, controls=56). The MEM integrates regional activation levels and pairwise correlation-based functional connectivity (FC), providing the potential for better characterization of clinically meaningful brain states and how they change over time. Using the HCP/Glasser atlas to define brain regions within the default mode (DMN) and dorsal attention (DAN) networks, group differences in regional activation, graph measures of FC, and MEM features such as transition rates between minima in an energy landscape along with correlations with cognitive and psychopathological measures were examined. Psychosis was associated with reduced activation in several regions and multiple FC graph metric alterations. MEM demonstrated a wider variety of DMN and DAN activation/deactivation configurations, with more frequent switching between them, more pronounced network configuration differences and higher basin transition rates with reduced basin dwell times suggesting temporally unstable network configurations, meaning the brain cannot rely on any particular configuration for cognitive processing. Activation of only three regions correlated with working memory, but none of the FC metrics did. MEM features, in particular basin transitions and total energy, correlated negatively with working memory. Our findings suggest that MEM provides unique information, specifically attenuated inter-network connectivity with reduced stability of DMN and DAN brain states, to characterize networks as targets and their features as markers for novel treatment development.

neuroscience↗

bioRxiv2023

Specific guidelines for time and space of multisensory plasticity in the superior colliculus.

The potential to combine facts from exceptional senses, and thereby facilitate detecting and localizing events, commonly develops regularly in cat superior colliculus (SC) neurons. Multisensory integration in SC neurons depends on the spatial and temporal relationships of cross-modal cues. Here, we reveal that the parallel process of short-term plasticity during adulthood that would adapt multisensory integration to reliable changes in environmental conditions. The short-term experience altered the temporal preferences of SC neurons, this short-term plasticity was limited to changes in cross-modal timing (a factor commonly induced by events at different distances from the receiver. Nonetheless the plasticity was no evident in response to changes in cross-modal spatial configuration.

neuroscience↗

bioRxiv2022

The microtubule-associated protein SlMAP70 interacts with SlIQD21 and regulates fruit shape formation in tomato

The shape of tomato fruits is closely correlated to microtubule organization and the activity of microtubule associated proteins (MAP), but insights into the mechanism from a cell biology perspective are still largely elusive. Analysis of tissue expression profiles of different microtubule regulators revealed that functionally distinct classes of MAPs are highly expressed during fruit development. Among these, several members of the plant-specific MAP70 family are preferably expressed at the initiation stage of fruit development. Transgenic tomato lines overexpressing SlMAP70 produced elongated fruits that show reduced cell circularity and microtubule anisotropy, while SlMAP70 loss-of-function mutant showed an opposite effect with flatter fruits. Microtubule anisotropy of fruit endodermis cells exhibited dramatic rearrangement during tomato fruit development, and SlMAP70-1 is likely implicated in cortical microtubule organization and fruit elongation throughout this stage by interacting with SUN10/SlIQD21a. The expression of SlMAP70 (or co-expression of SlMAP70 and SUN10/SlIQD21a) induces microtubule stabilization and prevents its dynamic rearrangement, both activities are essential for fruit shape establishment after anthesis. Together, our results identify SlMAP70 as a novel regulator of fruit elongation, and demonstrate that manipulating microtubule stability and organization at the early fruit developmental stage has a strong impact on fruit shape.

plant biology↗

bioRxiv2021

Endogenous RNA editing of a nuclear gene BOSS triggers flowering in tomato

RNA editing is defined as the production of transcripts with RNA sequences different from those of the DNA template. Most of previous RNA editing studies have focused on organelles, while RNA editing of nuclear transcripts is largely unknown. Here, we describe the first example of nuclear transcript RNA editing in plant, the BOSS RNA editing regulates tomato flowering. The SNP (SNP1) located in the 5UTR of BOSS gene (the Balancer of SP and SFT) is associated with tomato early flowering, and two transcripts of BOSS produced by SNP1 associated RNA editing show functional differentiation, where BOSS-{beta} transcript promotes flowering while BOSS- does not. Furthermore, these two transcripts of BOSS are shown to regulate SP (anti-florigen) pathway at transcription level in the shoot apical meristem (SAM). Our findings reveal a new layer of complexity in the control of plant stem cell proliferation and provide the evidence of RNA-editing of a single gene for flowering, suggesting that molecular breeding programs to increase the RNA-editing efficiency may improve the productivity of tomatoes and other agricultural organisms.

plant biology↗

bioRxiv2020

Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato

Tomato (Solanum lycopersicum) is a highly valuable vegetable crop and yield is one of the most important traits. Uncovering the genetic architecture of yield-related traits in tomato is critical for the management of vegetative and reproductive development, thereby enhancing yield. Here we perform a comprehensive genome-wide association study for 27 yield-related traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many reported and novel genes related to vegetative and reproductive development, were identified, and these loci explained an average of [~]8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection, especially during tomato improvement. Furthermore, a candidate gene, SlALMT15 that encodes an aluminum-activated malate transporter, was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation through increasing photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.

plant biology↗

bioRxiv2020

Chromosome-level genome assembly of the African pike, Hepsetus odoe

The order Characiformes is one of the largest components of the freshwater teleost fauna inhabiting exclusively in South America and Africa with great ecological and economical significance. Yet, quite limited genomic resources are available to study this group and their transatlantic vicariance. In this study we present a chromosome-level genome assembly of the African pike (Hepsetus odoe), a representative member of the African Characiformes. To this end, we generated 119, 11, and 67 Gb reads using the single tube long fragment read (stLFR), Oxford Nanopore, and Hi-C sequencing technologies, respectively. We obtained an 862.1 Mb genome assembly with the contig and scaffold N50 of 347.4 kb and 25.8 Mb, respectively. Hi-C sequencing produced 29 chromosomes with 742.5 Mb, representing 86.1% of the genome. 24,314 protein-coding genes were predicted and 23,999 (98.7%) genes were functionally annotated. The chromosomal-scale genome assembly will be useful for functional and evolutionary studies of the African pike and promote the study of Characiformes speciation and evolution.

genomics↗