Biology subjects

Yang, Y.-H.

Publications and source records attributed to Yang, Y.-H..

9 recordsLinked to original sources

bioRxiv2025

gAIRR-wgs: An Algorithm to Genotype T Cell Receptor Alleles Using Whole Genome Sequencing Data

T cell receptor (TR) genes, including variable (TR_V), diversity (TR_D), and joining (TR_J) segments, exhibit allelic diversity that is critical to adaptive immunity. Growing evidence has identified associations between TR genes and immune-related diseases. Germline variants may influence TR gene function and subsequent usage, highlighting the importance of accurate TR allele profiling. However, accurately identifying germline TR from standard WGS data remains challenging due to short read lengths, limited depth, and high sequence similarity. To address these challenges, we developed gAIRR-wgs, for WGS-based TR allele typing. By incorporating novel alleles from HPRC individuals, gAIRR-wgs exhibited excellent performance in allele calling, with F1 scores of 100.0% for TR_D, 99.8% for TR_J, and 98.3% for TR_V. Applying this pipeline to 1,492 individuals from the Taiwan Biobank (TWB), we identified 449 novel TR alleles, 277 of which overlapped with HPRC release 1 data of mixed ethnicity and are absent in the IMGT database. Further population comparison analysis revealed significant TR allele distribution differences across global populations, showing population-specific patterns and diversity variations between ethnic groups. We also discovered TWB-specific deletion polymorphisms affecting contiguous TRGV and TRBV genes, which are not recorded in the gnomAD database and undetected by standard structural variant callers, highlighting the need for tailored approaches to resolve complex immune gene regions. In conclusion, gAIRR-wgs enables accurate TR allele calling from standard WGS data using feasible computational resources and reveals substantial immunogenetic diversity in population cohorts.

bioinformatics↗

bioRxiv2025

Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

The adaptive immune receptor repertoire (AIRR), composed of V(D)J-recombined T cell receptors (TR) and immunoglobulins (IG), is central to adaptive immunity. Accurate AIRR profiling depends on a comprehensive and diverse germline gene set encoding AIRR (gAIRR). Furthermore, gAIRR alleles themselves are associated with immune-related phenotypes and diseases. However, for TR genes, the IMGT database - the primary gAIRR reference - has not been updated since 2020 and lacks sufficient population diversity and complete flanking sequences. To address these limitations, we investigated 47 high-quality genomes from the Human Pangenome Reference Consortium (HPRC) using the gAIRR Suite and identified 335 novel TR alleles - 305 TRV and 30 TRJ - representing 91.6% and 30.9% increases over IMGT records. All novel alleles were crosschecked using two orthogonal pipelines. We also established a comprehensive flanking sequence database, including recombination signal sequences (RSS). We have made all resources publicly available to support immunogenomics research and clinical applications.

genomics↗

bioRxiv2024

Innovative platelet-derived extracellular vesicle drug delivery system for the treatment of corneal neovascularization

Platelet-derived extracellular vesicles (PEVs) have drawn attention due to their multifunctionality, ease of procurement, and abundant supply from clinical-grade platelet concentrates. PEVs can be easily endocytosed owing to their lipid bilayer membrane and nanosized structure, thereby increasing the bioavailability and functionality of their therapeutic effects. PEVs also possess multiple trophic factors that make them effective therapeutic agents. Since nanomedicine offers advantages over traditional therapies for eye diseases by overcoming physical ocular barriers, PEVs combined with an anti-angiogenic agent, kaempferol (KM), were evaluated for their ability to inhibit abnormal vessel formation in the cornea. Characterization of the nanoparticles indicated successful preparation of KM- loaded PEVs (PEV-KM) with a mean diameter of [~]160 nm and an encapsulation efficiency of [~]61%. PEV-KM was efficiently internalized into human vascular endothelial cells, resulting in inhibited function, evidenced by lower wound closure rates, reduced tube formation capacity, and downregulation of angiogenesis-related gene expression. Moreover, prolonged ocular retention was observed followed by topical application of PEV and PEV-KM in mouse eyes. In an alkali-burned corneal neovascularization (CoNV) mouse model, PEV (1%) was found to reduce vessel formation in the injured cornea. PEV with KM (1% PEV with KM 6 {micro}g/mL) showed an even stronger effect in suppressing CoNV and reducing the expression of proangiogenic and inflammatory cytokines. Together, our data suggests that topical administration of PEVs or in combination with KM (PEV-KM) is a promising therapeutic for managing CoNV.

bioengineering↗

bioRxiv2023

Psychophysical measurement of perceived motion flow of naturalistic scenes

The neural and computational mechanisms underlying visual motion perception have been extensively investigated over several decades, but most studies have used simple artificial stimuli such as random-dot kinematograms. Thus, it remains difficult to predict how human observers perceive optical flows in complex natural scenes. Here, we report a novel method to measure, psychophysically, optical flows perceived by human observers watching naturalistic movies, and to reveal the characteristics of human motion perception via comparison of the measured perceived flow to the ground truths and model predictions. We selected movie clips from the MPI Sintel Flow Dataset, which contains open-source computer graphics animations with ground truths. To measure the perceived vectors at a spatiotemporal point, we flashed a small dot during presentation of a brief clip and asked the observers to adjust the speed and direction of a matching random-noise stimulus, to reproduce the vector at the flashed point. The proposed method adequately estimated perceived flow, and the estimated perceived vector also indicated flow illusions, i.e., consistent deviations from the ground truths, in various ways, depending on the stimulus patterns. Comparisons with the predictions of biologically motivated models and machine vision algorithms indicated that some flow illusions were attributable to lower-level factors such as spatiotemporal pooling and signal loss, but others reflected higher-level computations including coordinate transformations that cannot be precisely predicted by existing flow estimation models. Psychophysical measurement of the optical flows that humans perceive in realistic environments constitutes a promising paradigm for advancing our understanding of visual motion perception. Significance StatementThe basic approach to studying human vision is to analyze relationships among subjective perceptual experiences, responses of neural mechanisms, and predictions of computational models. Recent technical advances have enabled researchers to access large-scale neuronal responses and model predictions for complex sensory inputs. The data on human visual perception, however, cannot be easily scaled up. Accurate measurement of rich visual experiences when viewing natural scenes remains challenging. We thus devised a novel psychophysical method to measure optical motion flows perceived by humans. We successfully visualized human-perceived flows of complex naturalistic movies and show, for the first time, ways in which human-perceived naturalistic flows agree with, and deviate from, the physical ground truths and the predictions of various visual motion models.

neuroscience↗

bioRxiv2022

Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters

The one-carbon recursive ketoacid elongation pathway is responsible for making various branched-chain amino acids, aldehydes, alcohols, and acetate esters in living cells. Controlling selective microbial biosynthesis of these target molecules at high efficiency is challenging due to enzyme promiscuity, regulation, and metabolic burden. In this study, we present a systematic modular design approach to control proteome reallocation for selective microbial biosynthesis of branched-chain acetate esters. Through pathway modularization, we partitioned the branched-chain ester pathways into four submodules including keto-isovalerate submodule for converting pyruvate to keto-isovalerate, ketoacid elongation submodule for producing longer carbon-chain keto-acids, ketoacid decarboxylase submodule for converting ketoacids to alcohols, and alcohol acyltransferase submodule for producing branched-chain acetate esters by condensing alcohols and acetyl-CoA. By systematic manipulation of pathway gene replication and transcription, enzyme specificity of the first committed steps of these submodules, and downstream competing pathways, we demonstrated selective microbial production of isoamyl acetate over isobutyl acetate. We found that the optimized isoamyl acetate pathway globally redistributed the amino acid fractions in the proteomes and required up to 23-31% proteome reallocation at the expense of other cellular resources, such as those required to generate precursor metabolites and energy for growth and amino acid biosynthesis. The engineered strains produced isoamyl acetate at a titer of 8.8 g/L (> 0.25 g/L toxicity limit), a yield of 0.17 g/g (47% of maximal theoretical value), and 86% selectivity, achieving the highest titers, yields and selectivity of isoamyl acetate reported to date.

synthetic biology↗

bioRxiv2020

Impact of conscious awareness on pupillary response to faces

Pupillary response reflects not only ambient light changes but also top-down factors. Nevertheless, it remains inconclusive whether the conscious awareness modulates the pupillary response. We investigated pupillary responses to faces under different conscious conditions using continuous flash suppression (CFS). In Experiment 1 and 2, we used a breaking-CFS procedure in which participants had to detect the face from suppression. Results showed that the pupil constricted more to upright faces than to inverted faces before the face was detected, suggesting that pupillary responses reflect face processing entering consciousness. In Experiment 3 and 4, we used a fixed duration-CFS procedure with both objective performance and subjective reports. Different pupillary responses were observed only when the participant was aware of the face. These findings imply that the conscious awareness is critical for modulating autonomic neural circuits of the pupillary function. The corresponding pupillary responses may reflect dynamic processes underlying conscious awareness.

neuroscience↗

bioRxiv2020

The potential SARS-CoV-2 entry inhibitor

Outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan and has rapidly spread to almost all parts of world. In coronaviruses, the receptor binding domain (RBD) in the distal part of S1 subunit of SARS-CoV-2 spike protein can directly bind to angiotensin converting enzyme 2 (ACE2). RBD promote viral entry into the host cells and is an important therapeutic target. In this study, we discovered that theaflavin showed the lower idock score (idock score: -7.95 kcal/mol). To confirm the result, we discovered that theaflavin showed FullFitness score of -991.21 kcal/mol and estimated {Delta}G of -8.53 kcal/mol for the most favorable interaction with contact area of SARS-CoV-2 RBD by SwissDock service. Regarding contact modes, hydrophobic interactions contribute significantly in binding and additional hydrogen bonds were formed between theaflavin and Arg454, Phe456, Asn460, Cys480, Gln493, Asn501 and Val503 of SARS-CoV-2 RBD, near the direct contact area with ACE2. Our results suggest that theaflavin could be the candidate of SARS-CoV-2 entry inhibitor for further study.

bioinformatics↗

bioRxiv2020

Naringenin as an antibacterial reagent controlling of biofilm formation and fatty acid metabolism in MRSA

MRSA is Methicillin-resistant Staphylococcus aureus and they are widespread and making trouble in treatment in communities and surgical areas. MRSA have been adapted to antibiotics so that they can block the access of antibiotics physically or chemically deactivate it or modify the precursor of the target. Flavonoids are secondary metabolites which are naturally produced by plant or fungus and they are acting generally as pigment, quorum sensing molecules, antibiotics to other competitive microorganisms. Their natural origins and multiple activities have drawn much attention to be developed as the potential drugs since flavonoids could be a good candidate to overcome antibiotic resistant bacteria. Among various flavonoids, we found out naringenin has antibacterial activity on MRSA and {Delta}agr mutants which are more resistance than MRSA to beta-lactam antibiotics by decreasing biofilm formation dramatically and decreasing the secretion of fatty acid. It also showed high synergetic activity with oxacillin to both antibacterial activity and biofilm inhibition. Considering the number of flavonoids, our experiments expand the possibility of the use of flavonoids to MRSA.

microbiology↗

bioRxiv2019

A key interfacial residue identified with in-cell structure characterization of a Class-A GPCR dimer

G protein coupled receptors (GPCRs) have been shown homo-dimeric. Despite extensive studies, no single residue has been found essential for dimerization. Lacking an efficient method to shift the monomer-dimer equilibrium also makes functional relevance of GPCR dimer elusive. Here, using fluorescence lifetime-based imaging for distance measurements, we characterize the dimeric structure of GPR17, a class A GPCR, in cells. The structure reveals transmembrane helices 5 and 6 the dimer interface, and pinpoints F229 a key residue, mutations of which can render GPR17 monomeric or dimeric. Using the resulting mutants, we show that GPR17 dimer is coupled to both Gi and Gq signaling and is internalized, whereas GPR17 monomer is coupled to Gi signaling only and is not internalized. We further show that residues equivalent to F229 of GPR17 in several other class A GPCRs are also important for dimerization. Our findings thus provide fresh insights into GPCR structure and function.

biochemistry↗