Biology subjects

Xia, X.-Q.

Publications and source records attributed to Xia, X.-Q..

6 recordsLinked to original sources

bioRxiv2025

Longitudinal Identification of Zebrafish Individuals by Deep Learning

The zebrafish (Danio rerio) is a critical vertebrate model organism in biomedical research. Accurate identification and longitudinal tracking of individual fish within cohorts enable linking genotype to complex phenotypes, essential for elucidating the molecular mechanisms underlying disease pathogenesis and trait formation. Nevertheless, the establishment of reliable long-term individual identification remains a significant challenge, primarily due to their diminutive size and minimal interindividual morphological variations. We developed ESC-IDNet, a dual-stage deep learning cascade architecture deployed on the FishIndivID platform (http://bioinfo.ihb.ac.cn/fishindivid), enabling high-precision identification. Trained and tested on [~]300,000 images from 450 zebrafish (31-122 dpf), our lateral body-based identification maintained >95% accuracy with updates only every 20 days, significantly outperforming dorsal head identification (requiring [~]13-day updates). Both views achieved 100% accuracy in 1-2 day tasks. ESC-IDNet surpassed alternatives in segmentation, alignment, feature extraction, and feature matching. This framework provides a robust, transferable paradigm for individual identification in fish species.

bioinformatics↗

bioRxiv2025

A real-time detection and non-destructive warning method for zebrafish body surface anomalies based on improved YOLOv8 framework

The detection of anomalies on fish surfaces is of critical importance for assessing fish health status, preventing fish disease outbreaks, predicting changes in water quality, enhancing fish welfare. The zebrafish (Danio rerio), a key model organism, has been increasingly utilized in various fields, including medicine, genetics and environmental toxicology. This has led to a corresponding increase in demand for intelligent management and detection systems. However, traditional methods of fish disease detection may have irreversible effects on fish, particularly small species, and often fail to meet the precision, non-destructive warning, and real-time requirements for zebrafish detection. To address this issue, this study proposes a novel method based on the YOLOv8 framework, designated ESC-YOLOv8-seg. This method significantly enhances the precision and speed of detecting surface abnormalities on small fish in complex settings by integrating the EMA the SPPELAN and C2f-Faster modules, and adding a detection head tailored for small targets. Furthermore, the integration of positional information and surface features enables the method to achieve real-time monitoring and non-destructive early warning of fish surface abnormalities. The proposed method enhances precision in small target detection and achieves high accuracy in discerning subtle differences among detection targets. In real aquaculture settings, it can reach an average speed of 106 FPS with a detection accuracy of 98%. Although this study has been designed to meet the specific needs of zebrafish scientific research, it is highly generalisable and can be applied to the real-time detection of underwater surface abnormalities in a range of fish species in aquaculture.

bioinformatics↗

bioRxiv2024

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

In terms of the utilization of omics data, the current fish database analysis functions are primarily relatively simple tools at the transcriptional level, aimed at obtaining the co-expression levels of specified genes or the data visualization of multiple genes, and do not enable users to perform comprehensive omics data analysis. Furthermore, the gene-level information currently provided by these multispecies fish genomics databases is incomplete, and there is a lack of a comprehensive portal that can offer multidimensional genetic information. To address these challenges, we collected extensive multi-omics information on 35 fishes and established the primary comprehensive multi-omics data information platform for fish, FishCODE (http://bioinfo.ihb.ac.cn/fishcode). We have collected experimental background of dataset which pertaining to the target fishes, selected a range of datasets that encompass a broad spectrum of research areas, and downloaded the corresponding raw omics data from public repositories such as the Sequence Read Archive (SRA). Through a unified pipeline analysis, FishCODE contains 11,216 samples from 540 sets of genomic, transcriptomic, and methylomic datasets. These data encompass transcript structure and expression, gene methylation levels, protein domains, protein subcellular localization, protein interactions, best matched protein (Swiss-Prot), associated SNP site information (47,111,018), orthologous genes, phylogenetic tree and GO/KEGG annotations. To facilitate comparison, we annotated the experimental background data sets of the FishCODE, FishGET, PhyloFish, FishSED and FishSCT databases using the Fish Experimental Condition Ontology. Currently, the FishCODE database omics dataset includes 146 unique experimental condition words, 654 cumulative experimental condition words, and 13 species with rich experimental background (more than 20 unique FECO words). These data are 3.5 times (42), 8.3 times (74), and 6.5 times (2) those of the second-ranked databases respectively. We generated word cloud maps for the experimental condition vocabularies of FishCODE and FishGET, illustrating the superior richness of FishCODEs experimental background.

bioinformatics↗

bioRxiv2022

FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome

With the advancement of single-cell sequencing technology in recent years, an increasing number of researchers have turned their attention to the study of cell heterogeneity. In this study, we created a fish single-cell transcriptome database centered on zebrafish (Danio rerio). FishSCT currently contains single-cell transcriptomic data on zebrafish and 8 other fish species. We used a unified pipeline to analyze 129 datasets from 44 projects from SRA and GEO, resulting in 964/26,965 marker/potential marker information for 245 cell types, as well as expression profiles at single-cell resolution. There are 117 zebrafish datasets in total, covering 25 different types of tissues/organs at 36 different time points during the growth and development stages. This is currently the largest and most comprehensive online resource for zebrafish single-cell transcriptome data, as well as the only database dedicated to the collection of marker gene information of specific cell type and expression profiles at single-cell resolution for a variety of fish. A user-friendly web interface for information browsing, cell type identification, and expression profile visualization has been developed to meet the basic demand in related studies on fish transcriptome at the single-cell resolution.

bioinformatics↗

bioRxiv2020

Integrative Transcriptomic Analysis Reveals the Immune Mechanism for A CyHV-3-Resistant Common Carp Strain

Anti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Virus challenging studies suggested that a breeding strain of common carp is resistant to this disease. This study illustrates the immune mechanisms involved in anti-CyHV-3 ability. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was performed. Tissues from the head kidney of common carp were extracted at day 0 (the healthy control) and day 7 after CyHV-3 infection (the survivors), and used to analyze the transcriptome through both Illumina and PacBio sequencing. Following analysis of the GO terms and KEGG pathways involved, the immune-related terms and pathways were merged. In order to dig out details in the immune aspect, The DEGs were filtered using the current common carp immune gene library. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-XSexpression network analysis was used to reveal the regulation of immune genes by lncRNA. The results demonstrated that the breeding carp strain develops marked resistance to CyHV-3 through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and MUC3. Moreover, the immune suppressive signals, such as suppression of IL21R on STAT3, PI3K mediated inhibition on inflammation by dopamine upon infection, as well as the inhibition of NLRC3 on STING during a steady state. Possible susceptible factors for CyHV-3, such as ITGB1, TLR18, and CCL4, were also revealed from the non-breeding strain. The results of this study also suggested that Nramp and PAI regulated by LncRNA could facilitate virus infection and proliferation for infected cells respectively, while T cell leukemia homeobox 3 (TLX3) as well as galectin 3 function by lncRNA may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.

immunology↗

bioRxiv2019

Global gene expression profile during low temperature in the brain of grass carp (Ctenopharyngodon idellus)

Grass carp is an important commercial fish widely cultured in China. Large range of temperature, in particular extremely low temperature, has dramatic effects on the aquaculture of this teleost. However, there is relatively little research on the molecular responses in the fish exposed to cold. Given the limited vision of approaches targeting individual genes, we investigated the transcriptome profiles of brain in response to cold in order to comprehensively characterize molecular mechanisms behind it. This study indicated that the estrogen signaling pathway was inhibited in brain when grass carp acclimated to low temperature, while terpenoid backbone biosynthesis pathway and steroid biosynthesis pathway were significantly activated. Such a result implied the crucial role of cholesterol in cold acclimation. Moreover, plenty of differentially expressed genes associated with spliceosomes were enriched during cooling process, which suggested alternative splicing may be involved in the regulation of biological process in acclimation to temperature changes. In researches on extremely low-temperature tolerance, we identified four genes (DUSP1, HSPA6, NR4A1 and GADD45B) associated with MAPK signaling pathway. The four genes, extensively up-regulated at 4{degrees}C and remained relatively low expression at moderate temperature, were closely related with extremely cold condition. Further examination of the candidate genes can provide insights into the mechanisms of grass carp to endure extremely low temperature in the winter.

zoology↗