Biology subjects

Liu, J.-Y.

Publications and source records attributed to Liu, J.-Y..

12 recordsLinked to original sources

bioRxiv2026

Task-Dependent Modulation of Feedback Control in Human Steering

We examined whether human steering behavior conforms to optimal feedback control (OFC) principles when driving a vehicle through sequences of upcoming gates varying in width (narrow/wide) relative to the vehicles size, while occasional lateral velocity perturbations elicited corrective steering responses. In 24 participants, three predictions of OFC were tested: (1) greater positional variability when passing wide gates; (2) reduced corrective steering (lower feedback gains) to perturbations for wide compared to narrow gates (minimum intervention); and (3) modulation of feedback gains according to the relative spatial configuration of upcoming gates. Steering data were analyzed in terms of vehicle position and control velocity, the latter representative of feedback gain modulations. Results supported all predictions. When no perturbations occurred, participants showed wider distributions of passing locations through wide gates, consistent with allowing more task-relevant variability. During perturbed trials, feedback gains were lower for wide gates, confirming context-dependent control. When both gate types were center aligned, feedback responses were symmetric, whereas alignment of inner posts produced asymmetric feedback gains, being stronger for outward perturbations in narrow gates. Overall, these findings indicate that participants adapt their feedback control strategies to task-specific spatial constraints, demonstrating flexible optimization of steering control behavior.

neuroscience↗

bioRxiv2026

Repertoire-wide contextual mapping reveals signal functions in cooperatively breeding crows

Communication structures society, and is likewise shaped by relationships and shared tasks; yet, for most socially complex species, we know little of their full vocal repertoire and its functions. We investigated how communication structures the who, what, and when of social interactions in cooperative carrion crows - group-living birds who rely on coordinated behaviors, as in chick care. Leveraging machine learning to integrate large-scale data from crow-borne audio-loggers and nest cameras, we charted the vocal repertoire across 24 cooperative groups and mapped all discovered call types to behaviors and social context. We found that crows used a rich repertoire across three domains of joint behavior - flocking, chick care, and territorial display. Relatively quiet call types were abundant and included close-range calls that may coordinate chick care by announcing nest visits. Our study demonstrates how combining continuous-capture data and machine learning can reveal a holistic understanding of how vocalizations function across contexts.

animal behavior and cognition↗

bioRxiv2026

Zebra finch females flexibly communicate with each other and with AI-driven acoustic interaction models

Vocal interactions are fundamental for social functioning across animals, including humans. The diverse rules underlying these exchanges remain largely unknown, and emerging AI technologies offer promising avenues for investigation. We used computational tools to collect and analyze >1,000 hours of vocal interactions between female zebra finches and discovered that their interactions were characterized by correlated call production and structure, rapid acoustic modulation, and response selectivity. To test these interaction rules, we developed a generative audio large language model (ZF-AIM Acoustic Interaction Model) that engaged in real-time vocal exchanges with birds. When birds interacted with ZF-AIM, their vocal production and flexibility recapitulated key naturalistic features, which did not happen with non-interactive playbacks. Targeted ablations of ZF-AIM revealed that call timing and structure differentially contribute to natural vocal interactions. Using these AI-animal interactions, we demonstrate how AI can be leveraged to reveal fundamental rules underlying animal communication.

animal behavior and cognition↗

bioRxiv2025

Debutylation and Dephenylation of Organotin Compounds Through Fungal Laccase-Mediator Systems

In this study, the biodegradation of tetrabutyltin (TeBT) and tetraphenyltin (TePhT) through various laccase-mediator systems were investigated. The fungal laccases used were from the extracellular fluid of solid fermentation culture of white-rot fungi Perenniporia tephropora TFRI 707, Agrocybe aegerita, and Pleurotus geesteranus, with 2,2-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid), violuric acid, 4-hydroxyacetophenone, and syringaldehyde being used as mediators. After 7 days of incubation, 300 g/L of TeBT or 1000 g/L of TePhT were added, the laccase obtained from P. tephropora TFRI 707 removed 83.9%-87.4% of TeBT and 78.0%-91.9% of TePhT; the laccase obtained from A. aegerita removed 73.7%-88.9% of TeBT and 75.5%-92.0% of TePhT; and the laccase obtained from Pl. geesteranus removed 70.4%-85.3% of TeBT and 72.9%-90.2% of TePhT (percentages include incubation with and without mediators). Tributyltin (TBT), dibutyltin (DBT), and monobutyltin (MBT) were detected during the degradation of TeBT. Triphenyltin (TPhT), diphenyltin (DPhT), and monophenyltin (MPhT) were detected during the degradation of TePhT. Therefore, laccases can effectively and rapidly remove butyl or phenyl side chains from the organotin compounds. Because dealkylated alkyl organotin compounds and the elemental tin exhibit considerably low toxicity, laccases can potentially be used in environmental cleanup.

microbiology↗

bioRxiv2024

Visuoinertial and visual feedback in online steering control

Multisensory integration has primarily been studied in static environments, where optimal integration relies on the precision of the respective sensory modalities. However, in numerous situations, sensory information is dynamic and changes over time, due to changes in our bodily state and the surrounding environment. Given that different sensory modalities have different delays, this suggests that optimal integration may not solely depend on sensory precision but may also be affected by the delays associated with each sensory system. To investigate this hypothesis, participants (n = 22, 16 female) engaged in a continuous steering task. Participants sat on a motion platform facing a screen that displayed a cartoonish traffic scene, featuring a car traveling along a road. In the visuoinertial condition, where vestibular and somatosensory feedback were available, they were tasked with counteracting an external multi-frequency perturbation signal, which laterally perturbed the platform and the car, such that the car was kept within the center of the road. In the visual condition, the visual car was perturbed, while the motion platform remained stationary. We show that participants compensate better for the perturbation in the visuoinertial than the visual condition, particularly in the high frequency range of the perturbation. Using computational modelling, we demonstrate that this enhanced performance is partially due to the shorter delay of the vestibular modality. In this condition, participants rely more on the vestibular information, which is less delayed than the more precise but longer delayed, visual information. Author summaryNavigating the world effectively requires the continuous integration of sensory information related to our self-motion, forming a cohesive representation of our current location and direction. Although studies on multisensory integration indicate that sensory inputs are combined optimally based on their precision, these findings have largely been derived from static experimental settings. In real-life situations, the sensory environment changes continuously, as does the state of our body. In such scenarios, how are sensory inputs combined? We developed an experimental paradigm where participants were tasked with controlling a simple vehicle while counteracting a time-varying perturbation signal. To assess the role of different sensory inputs we manipulated whether visual and inertial (primarily vestibular) cues were available or solely visual cues. Our results show that the presence of both visual and inertial cues significantly improved task performance. Modeling suggests this improvement is likely due to the shorter delay associated with the vestibular system compared to the visual system. Collectively, our results suggest that sensory precision alone is insufficient for effective state estimation and control in naturalistic scenarios, where accounting for the different delays of the sensory systems is critical for optimal task performance.

neuroscience↗

bioRxiv2024

Developmental Stage and Cellular Context Determine Oncogenic and Molecular Outcomes of Ezh2Y641F Mutation in Hematopoiesis

Mutations in the histone methyltransferase EZH2, particularly the Y641 hotspot mutation, have been implicated in hematologic malignancies, yet the effect of timing and cellular context on their oncogenic potential has remained unknown. In this study, we utilized a conditional allele with tissue-specific Cre drivers to investigate the effects of Ezh2Y641F mutations at various stages of development, with a focus on the hematopoietic system. We found that ubiquitous heterozygous Ezh2Y641F expression at birth, or conditional expression in hematopoietic or mesenchymal stem cells, led to decreased survival due to hematopoietic defects and bone marrow failure, with no evidence of malignancy. In contrast, Ezh2Y641F expression in committed B cells drives lymphoma formation, highlighting the lineage-specific oncogenic activity of the mutation. Transcriptomic analysis of B cell progenitors revealed key pathway alterations between Cre models such as altered IL2-Stat5 signaling pathway, differential expression of E2F targets, and altered GTPase pathway expression driven by upregulation of Guanylate Binding Proteins (GBPs) in Mx1-Cre Ezh2Y641F pro-B cells. We further found that the GBP locus is regulated by Ezh2-mediated H3K27me3, it is associated with poorer survival in Acute Myeloid Leukemia patients and has variable effects on apoptosis in human lymphoma and leukemia cell lines. These findings suggest that the Ezh2Y641F mutation may alter immune regulatory pathways, cell differentiation and apoptosis, with potential implications for disease progression. Our results highlight the critical role of mutation timing and cellular context in EZH2-driven hematopoietic disease, resulting in distinct downstream changes that shape the oncogenic impact of EZH2.

cancer biology↗

bioRxiv2024

Gap-App: A sex-distinct AI-based predictor for pancreatic ductal adenocarcinoma survival as a web application open to patients and physicians

Withdrawal StatementThe authors have withdrawn this manuscript because the final version, now accepted by Cancer Letters, underwent substantial revisions during peer review that significantly changed the conclusions of the study. The AI models deployed are entirely different from those in the preprint, and the performance metrics originally reported (e.g., accuracy, precision) are no longer valid. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

bioinformatics↗

bioRxiv2023

A Superior Thumb Drive: Optimizing DNA Stability for DNA Data Storage

DNA digital data storage is an emerging technology with the potential to keep up with increasing demands in space, energy, and materials used for information storage. To make DNA storage systems more practical and cost-effective, it is crucial to determine how the physical and chemical properties of DNA affect its performance. Thus far, scientists have experimented with various DNA storage mediums and encoding techniques to maintain DNA stability. In this study, we first review existing strategies for maintaining DNA stability under various environmental constraints, organized according to the application of the storage system (Archival Storage, Working Storage, and Dynamic Storage). Then, we report on our own quantitative evaluation of the tradeoffs between storage density and DNA stability to identify the optimal system configurations for distinct storage scenarios.

bioinformatics↗

bioRxiv2022

Death-seq identifies regulators of cell death and senolytic therapies

Selectively ablating senescent cells ("senolysis") is an evolving therapeutic approach for age-related diseases. Current senolytics are limited to local administration by potency and side effects. While genetic screens could identify senolytics, current screens are underpowered for identifying genes that regulate cell death due to limitations in screen methodology. Here, we establish Death-seq, a positive selection CRISPR screen optimized to identify enhancers and mechanisms of cell death. Our screens identified synergistic enhancers of cell death induced by the known senolytic ABT-263, a BH3 mimetic. SMAC mimetics, enhancers in our screens, synergize with ABT-199, another BH3 mimetic that is not senolytic alone, clearing senescent cells in models of age-related disease while sparing human platelets, avoiding the thrombocytopenia associated with ABT-263. Death-seq enables the systematic screening of cell death pathways to uncover molecular mechanisms of regulated cell death subroutines and identify drug targets for diverse pathological states such as senescence, cancer, and neurodegeneration.

cell biology↗

bioRxiv2022

High efficiency multiplex biallelic heritable editing in Arabidopsis using an RNA virus

Delivery of gene editing components such as the Cas nuclease and single guide RNAs (sgRNAs) into plant cells is commonly accomplished by agrobacterium-mediated transformation. Although Arabidopsis is easy to transform, generation of biallelic edited plants requires screening a large number of plants in subsequent generations. Here, we describe optimization of the Tobacco rattle virus (TRV) for in planta delivery of sgRNAs fused to a tRNAIleu that induces efficient multiplex somatic and biallelic heritable editing in Arabidopsis. Inclusion of tRNAIleu enhances the systemic movement of TRV and the mutant phenotype is visible in the initial TRV::sgRNA-tRNAIleu infected Arabidopsis, which allows for the uncovering of lethal phenotypes. Mutant progeny are recovered in the next generation (M1) at frequencies ranging from 30-60%, with 100% mutant recovery in the following (M2) generation. TRV::tRNAIleu system described here allows generation of biallelic edited plants in a single generation and is amenable for large-scale high throughput CRISPR screens.

plant biology↗

bioRxiv2020

The Genomic Formation of Human Populations in East Asia

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE - 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to [~]3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.

genomics↗

bioRxiv2018

Bradyrhizobium diazoefficiens USDA 110-Glycine max interactome provides candidate proteins associated with symbiosis

Although the legume-rhizobium symbiosis is a most important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog and domain-based approaches, we constructed an inter-species protein interactome with 5115 protein-protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was validated by expression pattern analysis in nodules, GO term semantic similarity, and co-expression analysis. One sub-network was further confirmed using luciferase complementation image assay. In the G. max-B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top ten highly interacting proteins (hubs) for each of the two species. KEGG pathway analysis for each hub showed that two 14-3-3 proteins (SGF14g and SGF14k) and five heat shock proteins in G. max are possibly involved in symbiosis, and ten hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related SNARE proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome and symbiosis proteins provide a valuable basis for understanding the molecular mechanism of root nodule symbiosis in soybean.

bioinformatics↗