Biology subjects

Yang, C.-J.

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

5 recordsLinked to original sources

bioRxiv2026

High culturable diversity and climate-associated seasonal dynamics of Saccharomycotina yeasts in subtropical forest leaf litter

Forest-associated Saccharomycotina occur at low relative abundance, limiting inference about their diversity and dynamics. We sampled leaf litter weekly for 47 weeks across a subtropical forest in northern Taiwan. Enrichment, isolation and ITS sequencing recovered 687 isolates, including 613 Saccharomycotina representing 56 described species and 77 putatively novel operational taxonomic units. Rarefaction indicated unsampled culturable diversity. Among litter traps, community dissimilarity was high and dominated by taxon replacement, but neither topography nor geographic distance was associated with composition, and turnover matched randomised expectations. Richness peaked during warm, wet periods and declined in winter, and minimum temperature showed the strongest statistical association. Composition was associated with maximum temperature, minimum relative humidity, precipitation and solar radiation. Selected isolates' thermal optima covaried with collection-week temperatures, and two October Magnusiomyces magnusii isolates had higher optima than four winter isolates. Together, these findings reveal substantial culturable diversity and seasonal community restructuring consistent with temperature-related filtering.

microbiology↗

bioRxiv2026

A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae

Saccharomyces cerevisiae predominantly exists as diploid cells in nature, a life-cycle feature that limits classical genetic analyses of wild populations. Here, we establish a stable haploid strain collection derived from 33 diverse Taiwanese S. cerevisiae isolates through targeted disruption of the HO endonuclease gene. This resource spans predomesticated Asian wild lineages and enables systematic analyses of mating compatibility, reproductive isolation, and ecological trait variation. Although all pairwise hybridizations formed zygotes, many produced low spore viabilities, revealing strong postzygotic barriers. Genome analyses show that reduced hybrid fertility is primarily associated with chromosomal inversions and inter-chromosomal rearrangements rather than sequence divergence, indicating that structural variation maintains lineage separation despite geographic coexistence. Phenotypic profiling uncovered marked ecological differentiation, with the most diverged TW1 lineage favoring cooler growth conditions and a naturally occurring hybrid exhibiting heterosis with expanded thermal tolerance. While most wild strains grew poorly on maltose, two anthropogenically associated strains displayed enhanced maltose utilization linked to functional MAL regulatory alleles and maltose-specific transporters. Together, these findings demonstrate how structural genomic variation and metabolic gene divergence drive ecological and reproductive divergence in wild S. cerevisiae and establish this haploid collection as a platform for studying yeast evolution in nature.

genetics↗

bioRxiv2025

Dynamic evolution of AT-rich isochores shapes the genome of an intertidal fungus Annulohypoxylon annulatoides

Marine and coastal fungi experience intense environmental variability, yet the genomic mechanisms enabling filamentous fungi to tolerate such conditions remain unclear. From 56 fungal isolates collected along the Lailai rocky shore in northern Taiwan, we selected Annulohypoxylon annulatoides for deeper investigation due to its prevalence and distinctive stress response. Phenotypic assays revealed that this strain exhibits distinct growth and recovery dynamics under salinity, temperature, and UV stress compared to conspecific strains isolated from tree bark. To investigate the genomic basis of its adaptation, we generated a high-quality 41.8 Mbp de novo genome assembly with 11,529 predicted proteins. Across Hypoxylaceae genomes, we identified variably sized and dispersed AT-rich isochores, which in A. annulatoides were enriched in repeats and displayed low gene density. Despite differences in AT content, core gene content and Pfam domain profiles remained conserved. These AT-rich isochores exhibit several sequence and structural features consistent with scaffold/matrix attachment regions (S/MARs), raising the possibility that they influence higher-order genome organisation. Comparative analyses suggest they arose through independent repeat insertions or via ancestral repeat amplifications. Together, our findings point to a role for AT-rich isochores in shaping genome architecture and potentially mediating stress-responsive regulation, supporting the broader environmental flexibility observed in Hypoxylaceae, including adaptation to dynamic coastal habitats.

genomics↗

bioRxiv2019

TAO Kinase 3 Overexpression Is a Poor Prognosis Marker for Lung Adenocarcinoma and Predicts Paclitaxel Resistance

High expression of TAOK3 has been observed in several cancers, but very little about TAOK3-involved mechanisms has been reported. In this study, we investigated the role of TAOK3 in the therapeutic effect of paclitaxel treatment. Protein expression of TAOK3 was evaluated among 121 patients by using immunohistochemical staining. TAOK3 expression was estimated by analyzing the genes expression and its correlation with the IC50 of paclitaxel in cells. The expression of TAOK3 in lung cancer was highly correlated with poor overall survival, progression-free survival, and recurrence rate in lung cancer patients. The expression level of TAOK3 was positively correlated with paclitaxel resistance in the lung cancer cell lines. The depletion of TAOK3 could enhance the sensitivity of paclitaxel in lung cancer and vice versa. TAOK3 expression is associated with paclitaxel-resistance and could be a clinical predictor for disease recurrence and a potential therapeutic target in lung cancer.

cancer biology↗

bioRxiv2017

Adenylate kinase-4 modulates oxidative stress and stabilizes HIF-1α to drive lung cancer metastasis

Disrupting signaling axes that are essential for tumor metastasis may provide therapeutic opportunity to cure cancer. We previously identified adenylate kinase 4 (AK4) as a biomarker of metastasis in lung cancer. Here we analyze AK4-associated metabolic gene signature and reveal HIF-1 is transcriptionally activated and associated with poor prognosis in lung adenocarcinoma patients. Overexpression of AK4 shifts metabolism towards aerobic glycolysis and elevates intracellular reactive oxygen species (ROS), which stabilizes and exaggerates HIF1- protein expression and concurrently drives epithelial-to-mesenchymal transition (EMT) in hypoxia. Furthermore, overexpression of AK4 reduces hypoxic necrosis in tumors and promotes liver metastasis in vivo. Connectivity map analysis of AK4 gene signature identifies Withaferin-A as a potential compound to inhibit AK4-HIF-1 signaling axis, which then shows promising anti-metastatic potency in an orthotopic xenograft model of lung cancer. Our findings offer an alternative strategy to impair lung cancer metastasis via targeting AK4-HIF-1 axis.

cancer biology↗