Biology subjects

Yang, J.-B.

Publications and source records attributed to Yang, J.-B..

6 recordsLinked to original sources

bioRxiv2026

Identification of Mitochondrial-Lipid Metabolism-Related Diagnostic Targets in Osteoarthritis: Integrative Multi-omics Data and Experimental Validation

Objective: Osteoarthritis (OA) is a degenerative joint disease associated with metabolic dysregulation. This study aims to identify mitochondrial-lipid metabolism-related hub genes and explore their mechanisms in OA. Methods: Training (GSE55235) and validation (GSE55457 and GSE82107) cohorts were retrieved from the Gene Expression Omnibus (GEO) database. Candidate genes were derived by overlapping differentially expressed genes, mitochondrial-lipid metabolism-related genes, and weighted gene co-expression network analysis module genes. Machine learning algorithms were applied to screen hub genes. The diagnostic performance, functional pathways, immune infiltration, regulatory networks, drug interactions, and molecular docking of the hub genes were systematically evaluated. An interleukin-1{beta}-stimulated chondrocyte OA model was assayed for cell viability, interleukin-6 (IL-6), apoptosis, and hub-gene expression via Cell Counting Kit-8, enzyme-linked immunosorbent assay, flow cytometry, and reverse transcription-polymerase chain reaction. Results: Twenty-five candidate genes were screened, from which six hub genes (alpha-methylacyl-CoA racemase [AMACR], uncoupling protein 2 [UCP2], acyl-CoA thioesterase 7 [ACOT7], aldehyde dehydrogenase 3 family member A2 [ALDH3A2], armadillo repeat containing X-linked 2 [ARMCX2], and monoamine oxidase A [MAOA]) were further identified. The six hub genes exhibited robust diagnostic ability in the training cohort, correlated with immune-cell infiltration, and participated in lipid-metabolism pathways. In the OA model, chondrocyte viability was reduced, while IL-6 levels and apoptosis rate were elevated; five hub genes were markedly upregulated, whereas MAOA was significantly downregulated. Conclusion: Mitochondrial-lipid metabolism-related hub genes may serve as potential diagnostic biomarkers for OA, providing new insights into OA pathogenesis and potential therapeutic targets.

cell biology↗

bioRxiv2025

CASTLE: a training-free foundation-model pipeline for cross-species behavioral classification

Accurately and efficiently quantifying animal behavior at scale without intensive manual labeling is a long-standing challenge for neuroscience and ethology. Keypoint-based tracking emphasizes simplicity and efficiency but loses the richness of posture and context, while emerging foundation models capture pixel-level details, yet often require nontrivial efforts of retraining and can be more sensitive to backgrounds or lighting. Here, we present CASTLE, a training-free pipeline that addresses all these issues by synergistically combining foundation models for segmentation, tracking, and feature extraction. By isolating regions-of-interest (ROI), CASTLE first generates "focused (ROI-masked)" and orientation-invariant latent features, capturing rich postural details in zero-shot, fine-tuning-free manners. Following ROI isolation, CASTLE, through an interactive "Behavior Microscope" module, supports hierarchical clustering, for progressive, human-in-the-loop embedding and clustering. This enables raw-image-assisted discovery of behavioral classes without predefined categories. Across mice, Drosophila and C. elegans, CASTLE matches expert class annotations (>90%), reveals disease-relevant phenotypes in Parkinsonian mouse models. By eliminating purpose-specific model training and providing a raw-image-informed accessible workflow, CASTLE offers a scalable framework for interpretable, cross-species behavioral phenotyping.

neuroscience↗

bioRxiv2024

Bursts of rapid diversification, dispersals out of southern Africa, and two origins of dioecy punctuate the evolution of Asparagus

The genus Asparagus arose approximately 9-15 million years ago (Ma) and transitions from hermaphroditism to dioecy (separate sexes) occurred [~]3-4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus--first in a widely distributed Eurasian clade, then again in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also revealed several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes. Significance StatementAsparagus is an important model system for studying dioecy (separate sexes) evolution in plants. Asparagus taxonomy has been challenging, likely due to rapid species diversifications leading to highly variable species with complicated relationships that are impossible to resolve with limited DNA-sequence data. Using phylogenomics and the largest species sampling to date, we show that all Asparagus lineages originated from an initial radiation in southern Africa and that separate range expansions out of southern Africa set the stage for two distinct origins of dioecy in Asparagus. Our findings provide a deeper understanding of species diversification and the role of long-distance dispersals in the evolution of dioecy. This study also illustrates the utility of phylogenomics for elucidating past and present speciation processes.

evolutionary biology↗

bioRxiv2023

Single-Copy Orthologs (SCOs) improve species discrimination: A case study in subgus Jensoa (Cymbidium)

Standard barcodes and ultra-barcodes face challenges in delimitation and discrimination of closely related species with deep coalescence, hybrid speciation, gene flow or low sequence-variation. Single copy orthologs (SCOs) have been recommended as standardized nuclear markers in metazoan DNA taxonomy. Here, we assessed the performance of SCOs in identifying recently diverged species in subgenus Jensoa (Cymbidium) which has been poorly settled by ultra-barcode. More than 90% of target 9094 reference SCOs inferred from three genomes of Cymbidium were successfully retrieved for all 11 representative species in subg. Jensoa by ALiBaSeq from as low as 5x depth whole genome shotgun sequences. Species tree reconstructed from multiple refined SCO matrices under multispecies coalescent model successfully discriminated all species and discerned wrongly identified or labeled species. Plentiful and refined SCOs matrices obtained by implementing our pipeline facilitate not only phylogenetic study, but also high-resolution species diagnosing. Biparentally inherited SCOs as multi-locus marker not only advances the force of DNA barcoding, but also facilitates an eventual transition to species-tree-based barcoding strategies.

ecology↗

bioRxiv2021

Gene duplications and genomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the Tree of Life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation1, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here we examine the relationship of various facets of genomic evolution--including gene and genome duplication, genome size, and chromosome number--with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.

evolutionary biology↗

bioRxiv2018

GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data

GetOrganelle is a state-of-the-art toolkit to assemble accurate organelle genomes from NGS data. This toolkit recruit organelle-associated reads using a modified \"baiting and iterative mapping\" approach, conducts de novo assembly, filters and disentangles assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published samples, we reassembled the circular plastome in 47 samples using GetOrganelle, but only in 12 samples using NOVOPlasty. In comparison with published/NOVOPlasty plastomes, we demonstrated that GetOrganelle assemblies are more accurate. Moreover, we assembled complete mitogenomes of fungi and animals using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).

bioinformatics↗