Biology subjects

Tsai, C.-H.

Publications and source records attributed to Tsai, C.-H..

17 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

orthoSynAssign: refine orthogroups using synteny information

Accurately identifying orthogroups is crucial for precise phylogenetic reconstruction, but clustering-based methods often generate complex, many-to-many orthogroups that include confounding paralogs. Incorporating synteny offers a robust strategy to refine these clusters into high-granularity, single-copy orthologs. We introduce orthoSynAssign, a user-friendly, high-performance rewrite of the orthogroup refinement tool OrthoRefine, combining an intuitive Python interface with a core computing engine written in Rust. This hybrid architecture ensures straightforward installation, seamless data parsing, and exceptional computational efficiency. Evaluated against the Yeast Gene Order Browser (YGOB) dataset, orthoSynAssign demonstrated outstanding performance, substantially elevating the Area Under the Precision-Recall Curve. Furthermore, multi-threading benchmarks across 193 Eurotiomycetes genomes confirmed strong scalability, drastically reducing execution runtime while maintaining a strictly bounded, thread-independent memory footprint. Ultimately, orthoSynAssign provides a reliable and scalable framework for high-throughput phylogenomic workflows.

bioinformatics↗

bioRxiv2026

Denisovan leg bones from Taiwan reveal large body size

Denisovans are an extinct archaic Homo group whose lineage diverged from the Neanderthal lineage approximately 550,000 years ago and were widely distributed across eastern Asia until [~]45,000 years ago1-7. Their morphological features are known directly from the existing cranio- dental and phalangeal remains1,2,8-12. However, the body size and postcranial morphology of the Denisovans remain largely unknown. We here report that hominin femoral and tibial fossils recovered from the Penghu Channel, Taiwan, are Denisovans in their proteomic profiles. Morphologically, these specimens are among the largest leg bones known in Pleistocene Homo. They exhibit generally archaic features, but also show some modern human-like morphology, including a strong femoral pilaster. Our findings demonstrate that the Denisovan population at the northern circle had larger body size than earlier Homo erectus as well as Late Pleistocene Homo sapiens in eastern Asia. This challenges the generally held expectation that Pleistocene Homo followed Bergmanns rule that anticipates latitudinal decline of body size, and suggests that the large Denisovan brain resulted from their large body size at least partly. The strong pilaster developed in the Penghu femur suggests some behavioral similarities between the Denisovans and the Upper Palaeolithic modern humans and/or gene flow from the latter to the former.

paleontology↗

bioRxiv2026

Habitat and feeding ecology of a Denisovan from Late Pleistocene Taiwan

Denisovans, originally identified from ancient genome from Denisova Cave in Altai, were a sister group to the Neanderthals and were once widely distributed across diverse terrains in the north and south of eastern Asia1-5. Genomic studies suggest that there were multiple events of interbreeding between modern humans (Homo sapiens) and Denisovans somewhere in Asia6. However, little is known about Denisovan living environments, diet, ecological niche, the timing of their disappearance, and the possible coexistence with modern humans in different regions. Here we report the radiocarbon age and stable isotopic signature of Penghu 3, a large Denisovan tibia from Penghu Channel, Taiwan7. The results showed that Penghu 3 dates to approximately 45,000 years ago, the time when modern humans were already widespread in southern parts of Asia. This Denisovan individual inhabited a C4-dominated ecosystem, open environments such as savannahs and floodplains, or a mixture of both, and consumed a high proportion of animal protein similar to some European Neanderthals8-10, with no clear evidence for the use of aquatic resources. These findings have implications for the behavioral flexibility, large body size7, and eventual disappearance of the Denisovans.

paleontology↗

bioRxiv2026

The cap-independent translational regulation of NbRabGAP1 in Nicotiana benthamiana during BaMV infection

While cap-dependent translation is the eukaryotic norm, alternative pathways enable selective protein synthesis during stress. We describe a cap-independent mechanism regulating NbRabGAP1, a host factor essential for bamboo mosaic virus (BaMV) movement in Nicotiana benthamiana. The 5' untranslated region (5' UTR, 553-nt) of NbRabGAP1 contains three upstream open reading frames (uORFs) that typically hinder ribosome scanning. Using bicistronic reporter assays, we identified a functional internal ribosome entry site (IRES) within nucleotides 61-150. This IRES features a predicted stable Y-shaped RNA structure and a purine-rich R-motif. We demonstrate that NbPAB8, a poly(A)-binding protein, specifically binds this R-motif to enhance IRES-mediated translation over 2.5-fold. During BaMV infection, NbPAB8 expression is transiently upregulated, coinciding with maintained NbRabGAP1 levels despite potential repression of global cap-dependent translation. This represents a regulatory switch where viral infection triggers a PAB8-dependent IRES mechanism to sustain the vesicle trafficking machinery required for viral movement. Our findings reveal how viral stress rewires host translational control through specific RNA-protein interactions, ensuring the synthesis of critical host factors via IRES-mediated pathways. HighlightDuring bamboo mosaic virus infection, NbPAB8 binds a purine-rich IRES in the NbRabGAP1 5' UTR, bypassing global translation repression to maintain vesicle trafficking essential for viral movement.

molecular biology↗

bioRxiv2025

Long-term high throughput agitation culturing with real-time metabolic profiling

Cellular metabolism relies on the dynamic coordination between glycolytic flux in the cytosol and oxidative phosphorylation (OXPHOS) within the mitochondria. To study the metabolic profiles of cells, researchers apply a monitoring system for measurements of critical parameters, e.g., pH and dissolved oxygen (DO), to understand underlying energy production tendencies, dictating the performance, resilience and growth of cells. However, implementing sensitive, non-invasive sensors into long-term culturing environments remains a technical bottleneck. Here, we describe the DolphinQ bioanalyzer, a novel culturing platform designed for high-throughput, real-time monitoring of cellular metabolism states under physiologically relevant conditions. We validate the system across multiple cell types and experimental set-ups, demonstrating its ability to resolve subtle metabolic shifts that are typically obscured in end-point assays. Notably, we utilize the system to characterize the metabolic impact of heteroplasmy in a mitochondrial disease model with affected ATP synthase. Our results underscore the utility of continuous, minimally disruptive monitoring for revealing the complexities of cellular metabolic adaptation. The DolphinQ framework therefore offers a robust tool for optimizing culture conditions across a wide range of applications and advancing fundamental research into metabolic flux and mitochondrial dysfunction.

bioengineering↗

bioRxiv2025

Accelerating CHO-K1 Cell Line Development by Reducing Suspension Adaptation with a Microplate Agitation Culture System

Stable and productive CHO cell lines are essential for biopharmaceutical manufacturing, yet early expansion steps are often constrained by prolonged period required for suspension adaptation. Single-cell cloning (SCC) ensures monoclonality and regulatory compliance, but cells transitioning from static to suspension culture frequently exhibit variable recovery, which prolongs timelines and increases process variability. To address this challenge, mixing-based microplate culture systems have been developed to improve early expansion efficiency. The C.NEST platform provides controlled pneumatic mixing and environmental monitoring that facilitates earlier adaptation to suspension conditions. At the 96-well and 24-well stages, this system allows cells to establish stable growth under suspension-like environments, thereby shortening the adaptation period following transfer to shaking culture. In this study, we applied C.NEST to the SCC workflow for developing CHO-K1 stable cell lines. Integrating C.NESTs controlled mixing reduced adaptation time, enhanced the consistency of clone expansion, and improved the ability to identify high-yield clones. These findings highlight the potential of C.NEST to streamline cell line development workflows by accelerating early suspension adaptation and improving clone selection reliability. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/693844v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@ca76bforg.highwire.dtl.DTLVardef@3a3079org.highwire.dtl.DTLVardef@447e01org.highwire.dtl.DTLVardef@ac8d6f_HPS_FORMAT_FIGEXP M_FIG C_FIG C.NEST mixing shortens suspension adaptation, accelerates clone expansion, and enhances early-stage screening. HighlightO_LIThe C.NEST microplate agitation culture system accelerates early CHO-K1 cell line development. C_LIO_LIControlled pneumatic mixing improved oxygen transfer and medium homogeneity, promoting stable growth during early expansion. C_LIO_LIEarly mixing shortens suspension adaptation by approximately one week. C_LIO_LIMixing cultures enabled more accurate clone performance assessment, revealing high-producing outliers. C_LIO_LIC.NEST provides a scalable and reproducible solution for integrating mixing-based culture into single-cell cloning workflows. C_LI

cell biology↗

bioRxiv2025

Genomic rearrangements at the MAT locus suggest reproductive shifts in Rhodotorula yeasts

Transitions from canonical outcrossing to rare, cryptic, or noncanonical reproduction are widespread in fungi, but how mating-type (MAT) systems are reorganized at the genomic and population levels during these shifts remains unclear. The coexistence of sexually reproducing species and putatively asexual lineages makes Rhodotorula a natural comparative system for addressing this question. We analyzed 249 globally sampled strains using a combination of long-read and short-read sequencing. Phylogenomics resolved three major clades and several closely related species complexes. Chromosome-scale assemblies confirmed physical separation of the pheromone/receptor (P/R) and homeodomain (HD) loci, whereas non-random P/R-HD associations revealed constrained tetrapolar inheritance. The P/R locus showed conserved synteny within mating types but extensive structural divergence between A1 and A2 alleles, whereas the HD locus remained compact and conserved. Mating-type distributions varied across clades, with both A1 and A2 present in Clade C, lineage-structured partitioning in Clade B, and pronounced A2 dominance in Clade A. Genome-wide linkage disequilibrium (LD) decay in putatively asexual R. mucilaginosa, although slower than in sexual R. diobovata, was consistent with historical recombination in a species without an observed sexual cycle. Clade A further exhibited deep trans-specific polymorphism of STE3.A2 and relaxed purifying selection, mosaic A2 P/R configurations retaining RHA.A1, A1/A2 and A2/A2 hybrid genomes, and A2-associated gene content beyond MAT loci. In conclusion, our findings underscore the dynamic nature of MAT-locus remodeling in Rhodotorula and establish this genus as a valuable model for investigating transitions from heterothallism toward reproductive strategies less dependent on opposite-type partners.

evolutionary biology↗

bioRxiv2025

Phyling: phylogenetic inference from annotated genomes

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching a samples protein sequences against a Hidden Markov Models marker set, containing single-copy orthologs, retrieved from the BUSCO database. In the final step, users can choose between consensus and concatenation strategies to construct the species tree from the aligned orthologs. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed by protein sequences. The benchmark results show that Phyling substantially runs faster than OrthoFinder, a Reciprocal Best Hit based method, while achieving equal or better accuracy.

bioinformatics↗

bioRxiv2024

Distinct neuroendocrine subtypes predict treatment-induced neuroendocrine prostate cancer prognosis and provide clues for personalized treatment

Background and ObjectiveSecond-generation hormonal therapy inhibits castration-resistant prostate cancer (CRPC), but the tumor eventually recurs as neuroendocrine prostate cancer (NEPC) and turns lethal. Differentiating lineage plasticity that contributed to distinct NEPC subtypes aids in advancing treatments, particularly the recent FDA-approved 177Lu-PSMA-617 radiopharmaceutical therapy. MethodsWe integrated single-cell RNA sequencing data from fresh human CRPC cases. This comprehensive approach allowed us to identify distinct NEPC subpopulations and their respective lineage with high confidence. Key Findings and LimitationsWe uncovered N-Myc and REST as key transcription factors driving distinct neuroendocrine subtypes among 5,797 neuroendocrine-like epithelial cells in CRPC: a REST-dependent subtype (NE I), an N-Myc-dependent subtype (NE II), and a combined N-Myc/REST subtype (NE I+II). These subtypes were validated using multiplex immunofluorescence staining. Trajectory analysis of single-cell RNA sequencing data, along with multi-omics time course analysis of publicly available transcriptomic data recapitulated N-Myc and REST lineages. Additionally, we observed PSMA loss in N-Myc lineage NEPC and identified STMN1 as a biomarker for PSMA-negative subtype. We validated the prognostic value of STMN1 using the TCGA dataset and 60 in-house CRPC tissues. Given that surgery is rarely performed in advanced CRPC, leading to limited sample availability, further validation in larger cohorts is needed. Conclusions and Clinical ImplicationsAdeno-to-neuroendocrine lineage transition in prostate cancer leads to resistance to new therapies. The lethal NEPC phenotype should be revealed earlier in the disease course of patients with CRPC, providing crucial clues for personalized precision medicine.

cancer biology↗

bioRxiv2023

Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning

BackgroundAlternative splicing is a crucial mechanism of post-transcriptional modification responsible for the transcriptome plasticity and proteome diversity of a metazoan cell. Although many splicing regulations around the exon/intron regions have been discovered, the relationship between promoter-bound transcription factors and the downstream alternative splicing remains largely unexplored. ResultsIn this study, we present computational approaches to decipher the regulation relationship connecting the promoter-bound transcription factor binding sites (TFBSs) and the splicing patterns. We curated a fine data set, including DNase I hypersensitive sites sequencing and transcriptome in fifteen human tissues from ENCODE. Specifically, we proposed different representations of TF binding context and splicing patterns to tackle the associations between the promoter and downstream splicing events. Our results demonstrated that the convolutional neural network (CNN) models learned from the TF binding changes in the promoter to predict the splicing pattern changes. Furthermore, through an in silico perturbation-based analysis of the CNN models, we identified several TFs that considerably reduced the model performance of splicing prediction. ConclusionIn conclusion, our finding highlights the potential role of promoter-bound TFBSs in influencing the regulation of downstream splicing patterns and provides insights for discovering alternative splicing regulations.

bioinformatics↗

bioRxiv2022

Baculovirus Surface Display of Hemagglutinin and Neuraminidase for Monoclonal Antibody Production

The H7N9 influenza virus that emerged in 2013 is a dangerous infectious disease with a high mortality rate of up to 40%. Developing effective monoclonal antibodies (mAbs) to detect and treat the infection of this virus is therefore critical. In this study, we expressed hemagglutinin (HA) and neuraminidase (NA) of H7N9 (A/Anhui/1/2013) on the surface of baculovirus (i.e., HA7-Bac and NA9-Bac). Our results showed that both HA or NA proteins displayed on HA7-Bac or NA9-Bac could well maintain their native biological function. Mice antisera derived from the injections of either HA7-Bac- or NA9-Bac exhibited high inhibitory activity in the hemagglutination and neuraminidase assay of H7N9 virus. mAbs generated by immunization with HA7-Bac exhibited high neutralizing activity against H7N9 virus infectivity in cell assays, whereas mAbs generated by immunization with NA9-Bac inhibited neuraminidase activity. These results proved that baculovirus display of HA and NA from H7N9 could be convenient agents to generate neutralizing mAbs against virus infection.

bioengineering↗

bioRxiv2021

Volatility in coral cover erodes niche structure, but not diversity, in reef fish assemblages

Environmental fluctuations are becoming increasingly volatile in many ecosystems, highlighting the need to better understand how stochastic and deterministic processes shape patterns of commonness and rarity, particularly in high-diversity systems like coral reefs. Here, we analyze reef fish time-series across the Great Barrier Reef to show that approximately 75% of the variance in relative species abundance is attributable to deterministic, intrinsic species differences. Nevertheless, the relative importance of stochastic factors is markedly higher on reefs that have experienced stronger coral cover volatility. By contrast, -diversity and species composition are independent of coral cover volatility but depend on environmental gradients. Our findings imply that increased environmental volatility on coral reefs erodes assemblages niche structure, an erosion that is not detectable from static measures of biodiversity. One-Sentence SummaryCoral cover volatility modulates how stochastic and deterministic processes shape commonness and rarity in coral reef fishes.

ecology↗

bioRxiv2021

Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states

BackgroundMany long non-coding RNAs (lncRNAs) have been extensively identified in many higher eukaryotic species. The function of lncRNAs has been reported to play important roles in diverse biological processes, including developmental regulation and behavioral plasticity. However, there are no reports of systematic characterization of long non-coding RNAs in the fire ant Solenopsis invicta. ResultsIn this study, we performed a genome-wide analysis of lncRNAs in the brains of S. invicta from RNA-seq. In total, 1,393 novel lncRNA transcripts were identified in the fire ant. In contrast to the annotated lncRNA transcripts having at least two exons, novel lncRNAs are monoexonic transcripts with a shorter length. Besides, the transcriptome from virgin alate and dealate mated queens were analyzed and compared. The results showed 295 differentially expressed mRNA genes (DEGs) and 65 differentially expressed lncRNA genes (DELs) between virgin and mated queens, of which 17 lncRNAs were highly expressed in the virgin alates and 47 lncRNAs were highly expressed in the mated dealates. By identifying the DEL:DEG pairs with high association in their expression (Spearmans |rho| > 0.8 and p-value < 0.01), many DELs were co-regulated with DEGs after mating. Furthermore, several remarkable lncRNAs (MSTRG.6523, MSTRG.588, and nc909) that were found to associate with particular coding genes may play important roles in the regulation of brain gene expression in reproductive transition in fire ants. ConclusionThis study provides the first genome-wide identification of S. invicta lncRNAs in the brains in different reproductive states and will contribute to a fuller understanding of the transcriptional regulation underpinning reproductive changes.

genomics↗

bioRxiv2020

Inhibition of Severe Acute Respiratory Syndrome Coronavirus 2 main protease by tafenoquine in vitro

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the current pandemic, coronavirus disease 2019 (COVID-19), has taken a huge toll on human lives and the global economy. Therefore, effective treatments against this disease are urgently needed. Here, we established a fluorescence resonance energy transfer (FRET)-based high-throughput screening platform to screen compound libraries to identify drugs targeting the SARS-CoV-2 main protease (Mpro), in particular those which are FDA-approved, to be used immediately to treat patients with COVID-19. Mpro has been shown to be one of the most important drug targets among SARS-related coronaviruses as impairment of Mpro blocks processing of viral polyproteins which halts viral replication in host cells. Our findings indicate that the anti-malarial drug tafenoquine (TFQ) induces significant conformational change in SARS-CoV-2 Mpro and diminishes its protease activity. Specifically, TFQ reduces the -helical content of Mpro, which converts it into an inactive form. Moreover, TFQ greatly inhibits SARS-CoV-2 infection in cell culture system. Hence, the current study provides a mechanistic insight into the mode of action of TFQ against SARS-CoV-2 Mpro. Moreover, the low clinical toxicity of TFQ and its strong antiviral activity against SARS-CoV-2 should warrant further testing in clinical trials.

biochemistry↗

bioRxiv2020

Lipid Sponge Droplets as Programmable Synthetic Organelles

Living cells segregate molecules and reactions in various subcellular compartments known as organelles. Spatial organization is likely essential for expanding the biochemical functions of synthetic reaction systems, including artificial cells. Many studies have attempted to mimic organelle functions using lamellar membrane-bound vesicles. However, vesicles typically suffer from highly limited transport across the membranes and an inability to mimic the dense membrane networks typically found in organelles such as the endoplasmic reticulum. Here we describe programmable synthetic organelles based on highly stable nonlamellar sponge phase droplets that spontaneously assemble from a single-chain galactolipid and non-ionic detergents. Due to their nanoporous structure, lipid sponge droplets readily exchange materials with the surrounding environment. In addition, the sponge phase contains a dense network of lipid bilayers and nanometric aqueous channels, which allows different classes of molecules to partition based on their size, polarity, and specific binding motifs. The sequestration of biologically relevant macromolecules can be programmed by the addition of suitably functionalized amphiphiles to the droplets. We demonstrate that droplets can harbor functional soluble and transmembrane proteins, allowing for the co-localization and concentration of enzymes and substrates to enhance reaction rates. Droplets protect bound proteins from proteases, and these interactions can be engineered to be reversible and optically controlled. Our results show that lipid sponge droplets permit the facile integration of membrane-rich environments and self-assembling spatial organization with biochemical reaction systems. Significance statementOrganelles spatially and temporally orchestrate biochemical reactions in a cell to a degree of precision that is still unattainable in synthetic reaction systems. Additionally, organelles such as the endoplasmic reticulum (ER) contain highly interconnected and dense membrane networks that provide large reaction spaces for both transmembrane and soluble enzymes. We present lipid sponge droplets to emulate the functions of organelles such as the ER. We demonstrate that lipid sponge droplets can be programmed to internally concentrate specific proteins, host and accelerate biochemical transformations, and to rapidly and reversibly sequester and release proteins to control enzymatic reactions. The self-assembled and programmable nature of lipid sponge droplets will facilitate the integration of complex functions for bottom up synthetic biology.

synthetic biology↗

bioRxiv2018

An E3 ubiquitin ligase from Nicotiana benthamiana targets the replicase of Bamboo mosaic virus and restricts its replication

One upregulated host gene identified previously was found involved in the infection process of Bamboo mosaic virus (BaMV). The full-length cDNA of this gene was cloned by 5'- and 3'-rapid amplification of cDNA ends and found to encode a polypeptide containing a conserved RING-domain and a transmembrane domain. The gene might function as an E3 ubiquitin ligase. We designated this protein in Nicotiana benthamiana as ubiquitin E3 ligase containing RING-domain 1 (NbUbE3R1). Further characterization by using Tobacco rattle virus-based virus-induced gene silencing revealed an increased BaMV accumulation in both knockdown plants and protoplasts. To further inspect the functional role of NbUbE3R1 in BaMV accumulation, NbUbE3R1 was expressed in N. benthamiana plants. The wild-type NbUbE3R1-orange fluorescent protein (NbUbE3R1-OFP), NbUbE3R1/{bigtriangleup}TM-OFP (removal of the transmembrane domain) and NbUbE3R1/mRING-OFP (mutation at the RING domain, the E2 interaction site) were transiently expressed in plants. NbUbE3R1 and its derivatives all functioned in restricting BaMV accumulation. The common feature of these constructs was the intact substrate-interacting domain. Yeast two-hybrid and co-immunoprecipitation experiments used to determine the possible viral-encoded substrate of NbUbE3R1 revealed the replicase of BaMV as the possible substrate. In conclusion, we identified an upregulated gene, NbUbE3R1, that plays a role in BaMV replication.

microbiology↗