Biology subjects

Kwon, J. Y.

Publications and source records attributed to Kwon, J. Y..

8 recordsLinked to original sources

bioRxiv2026

Toward understanding drivers of specialized metabolism in Actinomycetota: insights from 1432 transcriptomics datasets for 132 strains

Actinomycetota are major sources of specialized metabolites with applications in drug discovery and agriculture, yet much of their biosynthetic potential remains silent under standard laboratory conditions. Limited understanding of the mechanisms controlling biosynthetic gene cluster (BGC) activation constrains metabolite discovery and production. Here, we generated 1432 RNA-seq datasets from 132 Actinomycetota strains grown in eight media to identify patterns associated with BGC expression. On average, strains expressed 44% of their encoded BGCs across the tested conditions, with more expression observed among known BGCs (61%) compared to uncharacterized BGCs (35%). Co-expression analyses revealed frequent associations between BGCs and transporters, transcriptional regulators, and proteins containing DUF397 and DUF742 domains. Targeted overexpression of candidate genes selected from BGC-associated co-expression modules increased metabolite production, with DUF397- and DUF742-containing operons showing the broadest effects by boosting the levels of several different specialized metabolites. Other genes boosted levels in a metabolite-specific manner. Together, our results support a multilayered model of BGC regulation in Actinomycetota in which BGC expression is shaped by medium composition, BGC-specific regulators, and integration of BGCs into broader transcriptional network modules. By connecting BGC expression to specific media and co-expressed genes, this study also provides a resource for selecting growth conditions and engineering specialized metabolism.

microbiology↗

bioRxiv2025

Can large language models reliably extract human disease genes from full-text scientific literature?

Manual extraction of high-fidelity gene-disease-phenotype information from human genetics literature is a labor-intensive task that requires trained human genetics researchers to read through many primary research papers. This presents a major challenge for maintaining up-to-date human disease genetic databases. Recent exploration into large language models (LLMs) opens new directions in automating this manual process. However, most approaches depend on pre-training, finetuning, or specialized generative artificial intelligence (GenAI) tools, but there is a lack of empirical evidence to show whether commercially-available LLMs can be directly used to reliably extract gene-disease-phenotype for human genetic diseases. Herein, we perform a benchmark of the use of three zero-shot prompted LLMs, namely GPT-4, DeepSeek and Claude, without task-specific fine-tuning, to extract human genetic information directly from full text of scientific papers. Using known congenital heart diseases (CHD) genes found in the open access CHDgene database (https://chdgene.victorchang.edu.au/) as the benchmark data set, GPT-4o achieved overall 88.8% extraction accuracy across 23 gene entries containing over 57 references, with 100% accuracy in gene name, 78.3% and 76.7% in disease and phenotype fields respectively. This work introduces a lightweight, easy-to-deploy, and yet robust LLM-based agent named GeneAgent, analyze sources of disagreement, and highlight the feasibility of integrating powerful LLM into genetic evidence synthesis workflows. Highlight- First systematic benchmark of LLMs for extracting human gene-disease-phenotype relationships from full-text biomedical articles - GeneAgent: a lightweight, highly accurate prompt-only LLM agent - New domain task-specific evaluation framework

bioinformatics↗

bioRxiv2024

Food texture preference reveals multisensory contributions of gustatory organs in behaviour and physiology

Food presents a multisensory experience, with visual, taste, and olfactory cues being important in allowing an animal to determine the safety and nutritional value of a given substance1. Texture, however, remains a surprisingly unexplored aspect, despite providing key information about the state of the food through properties such as hardness, liquidity, and granularity. Food perception is achieved by specialised sensory neurons, which themselves are defined by the receptor genes they express. While it was assumed that sensory neurons respond to one or few closely-related stimuli, more recent findings challenge this notion and support evidence that certain sensory neurons are more broadly tuned. In the Drosophila taste system, gustatory neurons respond to cues of opposing hedonic valence or to olfactory cues. Here, we identified that larvae ingest and navigate towards specific food substrate hardnesses, and probed the role of gustatory organs in this behaviour. By developing a genetic tool targeting specifically gustatory organs, we show that these organs are major contributors for evaluation of food texture and ingestion decision-making. We find that ablation of gustatory organs not only results in loss of chemosensation, but also navigation and ingestion preference to varied substrate textures. Furthermore, we show that certain neurons in the primary taste organ exhibit varied and concurrent physiological responses to mechanical and multimodal stimulation. We show that individual neurons house independent mechanisms for multiple sensory modalities, challenging assumptions about capabilities of sensory neurons. We propose that further investigations, across the animal kingdom, may reveal higher sensory complexity than currently anticipated.

neuroscience↗

bioRxiv2024

Drosophila HCN mediates gustatory homeostasis by preserving sensillar transepithelial potential in sweet environments

Establishing transepithelial ion disparities is crucial for sensory functions in animals. In insect sensory organs called sensilla, a transepithelial potential, known as the sensillum potential (SP), arises through active ion transport across accessory cells, sensitizing receptor neurons such as mechanoreceptors and chemoreceptors. Because multiple receptor neurons are often co-housed in a sensillum and share SP, niche-prevalent overstimulation of single sensory neurons can compromise neighboring receptors by depleting SP. However, how such potential depletion is prevented to maintain sensory homeostasis remains unknown. Here, we find that the Ih-encoded hyperpolarization-activated cyclic nucleotide gated (HCN) channel bolsters the activity of bitter-sensing gustatory receptor neurons (bGRNs), albeit acting in sweet-sensing GRNs (sGRNs). For this task, HCN maintains SP despite prolonged sGRN stimulation induced by the diet mimicking their sweet feeding niche, such as overripe fruit. We present evidence that Ih-dependent demarcation of sGRN excitability is implemented to throttle SP consumption, which may have facilitated adaptation to a sweetness-dominated environment. Thus, HCN expressed in sGRNs serves as a key component of a simple yet versatile peripheral coding that regulates bitterness for optimal food intake in two contrasting ways: sweet-resilient preservation of bitter aversion and the previously reported sweet-dependent suppression of bitter taste.

neuroscience↗

bioRxiv2023

Unilateral ephaptic program underlying sweetness dominance

In ephaptic coupling, physically adjacent neurons influence one anothers activity via the electric fields they generate. To date, the molecular mechanisms that mediate and modulate ephaptic couplings effects remain poorly understood. Here, we show that the hyperpolarization-activated cyclic nucleotide-gated (HCN) channel lateralizes the potentially mutual ephaptic inhibition between Drosophila gustatory receptor neurons (GRNs). While sweet-sensing GRNs (sGRNs) engage in ephaptic suppression of the adjacent bitter-sensing GRNs (bGRNs), HCN expression in sGRNs enables them to resist ephaptic suppression from the bGRNs. Such one-sided ephaptic inhibition confers sweetness dominance, facilitating ingestion of bitter-laced sweets. Flies with HCN-deficient sGRNs exhibited dramatically decreased attraction to sucrose mixed with moderate levels of caffeine, highlighting the behavioral significance that gustatory ephaptic inhibition promotes ingestion of carbohydrates buried in bitterness. Our findings indicate a role for the gating of ephaptic coding to ensure the intake of the essential nutrient despite bitter contaminants present in the feeding niche of Drosophila, as the gating establishes a hierarchy of gustatory neuron excitation. Such refinement provides a previously unappreciated mechanism for controlling the activity of a neuronal network with potential implications in the mammalian brain, given the evolutionary conservation of the HCN genes.

neuroscience↗

bioRxiv2022

Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation

The prevalence of highly repetitive sequences within the human Y chromosome has led to its incomplete assembly and systematic omission from genomic analyses. Here, we present long-read de novo assemblies of 43 diverse Y chromosomes spanning 180,000 years of human evolution, including two from deep-rooted African Y lineages, and report remarkable complexity and diversity in chromosome size and structure, in contrast with its low level of base substitution variation. The size of the Y chromosome assemblies varies extensively from 45.2 to 84.9 Mbp and include, on average, 81 kbp of novel sequence per Y chromosome. Half of the male-specific euchromatic region is subject to large inversions with a >2-fold higher recurrence rate compared to inversions in the rest of the human genome. Ampliconic sequences associated with these inversions further show differing mutation rates that are sequence context-dependent and some ampliconic genes show evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, the Yq12, is composed of alternating arrays of DYZ1 and DYZ2 repeat units that show extensive variation in the number, size and distribution of these arrays, but retain a 1:1 copy number ratio of the monomer repeats, consistent with the notion that functional or evolutionary forces are acting on this chromosomal region. Finally, our data suggests that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kbp distal to the currently established boundary. The availability of sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of specific traits with Y-chromosomal variants and garnering novel insights into the evolution and function of complex regions of the human genome.

genomics↗

bioRxiv2020

Multimodal and multisensory coding in the Drosophila larval peripheral gustatory center

The ability to evaluate food palatability is innate in all animals, ensuring their survival. The external taste organ in Drosophila larvae is composed of only few sensory neurons but enables discrimination between a wide range of chemicals and displays high complexity in receptor gene expression and physiological response profile. It remains largely unknown how the discrepancy between a small neuronal number and the perception of a large sensory space is genetically and physiologically resolved. We tackled dissection of taste sensory coding at organ level with cellular resolution in the fruit fly larva by combining whole-organ calcium imaging and single-cell transcriptomics to map physiological properties and molecular features of individual neurons. About one third of gustatory sense neurons responded to multiple tastants, showing a rather large degree of multimodality within the taste organ. Further supporting the notion of signal integration at the periphery, we observed neuronal deactivation events within simultaneous neighboring responses, suggesting inter-cellular communication through electrical coupling and thus providing an additional level in how neurons may encode taste sensing. Interestingly, we identified neurons responding to both mechanical and taste stimulation, indicating potential multisensory integration. On a molecular level, chemosensory cells show heterogeneity in neuromodulator expression. In addition to a broad cholinergic profile, markers on dopaminergic, glutamatergic or neuropeptidergic pathways are present either in distinct cell populations or are seemingly co-expressed. Our data further extend the sensory capacity of the larval taste system pointing towards an unanticipated degree of multimodal and multisensory coding principles.

neuroscience↗

bioRxiv2017

Multi-platform discovery of haplotype-resolved structural variation in human genomes

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, and strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three human parent-child trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs ([≥]50 bp) per human genome. We also discover 156 inversions per genome--most of which previously escaped detection. Fifty-eight of the inversions we discovered intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The method and the dataset serve as a gold standard for the scientific community and we make specific recommendations for maximizing structural variation sensitivity for future large-scale genome sequencing studies.

genomics↗