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Biology subjects

Lin, Y.

Publications and source records attributed to Lin, Y..

At least 19 recordsLinked to original sources

Widespread Presence of Catalytic RNAs in All Domains of Life

Very few ribozymes have been found in complex eukaryotes. Here, we developed a novel method, AbRiDGed, for highly accurate and sensitive ab initio self-cleaving ribozyme discovery. Our results indicate the existence of millions of self-cleaving ribozymes in humans and other species. We characterized ~150 novel classes of self-cleaving ribozymes, including one class which exhibits noncanonical biochemical properties and widespread presence in all domains of life and appears to play specific functions in complex organisms. These results revealed that the true complexity of the "ribozyme-ome" is several orders of magnitude higher than previously estimated. We demonstrate that newly identified self-cleaving ribozymes influence organismal fitness by regulating gene expression and enhancing transcriptome complexity in vivo. Moreover, these ribozymes hold promise as foundational tools for biotechnological applications, such as direct RNA detection technologies. Overall, catalytic RNAs are prevalent and diverse, and may represent a hidden regulatory layer in various organisms.

molecular biology↗

Heat-dependent engagement of a buried mitophagy motif in prohibitin 2

Mitophagy receptors are generally switched on by upstream enzymes rather than by the receptor itself. Whether a receptor can instead respond directly to a physical stimulus has not been established. Here we show that a second LC3-interacting region (LIR) in prohibitin 2 (PHB2) is regulated by temperature. It lies in a marginally stable helix that holds its two anchor residues about 5 angstrom apart, whereas a bound LIR spans about 9 angstrom. Replica-scaling simulations showed that this helix, but not a matched control from the same protein under identical scaling, samples that geometry; purified PHB2 bound ATG8-family proteins only at 313 K and above. Substitutions designed from this geometry to stabilise (K253A/R255A) or destabilise (I254G) the helix altered binding, mitochondrial recruitment and respiration in PHB2-null cardiomyocytes. Mice carrying the stabilising substitutions in cardiomyocytes sustained greater cardiac injury during heat stroke despite matched thermal load and comparable systemic injury. Motif accessibility may therefore be a regulated variable rather than a fixed property of a fold.

molecular biology↗

Acetylation of NDUFA13 at K7 Senses OXPHOS Dysfunction to Disrupt Prohibitin Scaffolds and Drive Cristae Remodelling in Heart Failure

Mitochondrial cristae disintegration is a hallmark of heart failure, yet how oxidative phosphorylation (OXPHOS) dysfunction triggers this structural collapse remains unclear. Here we identify acetylation of the complex I subunit NDUFA13 at lysine 7 (K7) as a metabolic sensor coupling OXPHOS dysfunction to cristae remodelling. OXPHOS inhibition drove NDUFA13-K7 hyperacetylation, inducing conformational compaction and translocation to the intermembrane space. Acetylated NDUFA13 competitively engaged PHB2 through its coiled-coil domain, displacing PHB1 and disassembling prohibitin scaffolds. The acetylation-mimetic NDUFA13-K7Q induced cristae fragmentation in vitro, and cardiomyocyte-specific K7Q knock-in mice showed accelerated mortality and cristae loss under pressure overload, accompanied by impaired TCA cycle flux, defective fatty acid oxidation and selective depletion of polyunsaturated cardiolipins. These findings establish NDUFA13-K7 acetylation as a reversible switch converting bioenergetic failure into pathological cristae remodelling and metabolic reprogramming, highlighting therapeutic potential for targeted deacetylation.

cell biology↗

Virtual lineages: in silico lineage tracing from single-cell and spatial transcriptomes

Experimental lineage tracing reveals histories and fates of individual cells but is costly and often impractical, particularly in primary human tissues. Gene expression differences that persist across cell divisions provide a basis for inferring ancestry from more accessible single cell transcriptomes, yet accurate lineage reconstruction remains challenging. Here, we introduce isCORAL, an in silico lineage-tracing framework that reconstructs clonal relationships and maps cell-fate dynamics from transcriptome snapshots alone. By identifying memory genes with heritable expression differences, isCORAL infers probabilistic clonal relationships and uses them to construct clone-oriented embeddings and dynamic cell-fate maps. Across diverse lineage-tracing datasets, isCORAL markedly outperforms tested alternatives in both memory-gene identification and lineage reconstruction. We use isCORAL to resolve early fate biases among transcriptionally similar hematopoietic stem cells and predict distinct developmental routes to shared outcomes. We extend isCORAL to spatial transcriptomics, validating inferred clonal relationships against an experimentally recorded lineage tree in mouse tumors and inferring early epiblast and amnion dynamics in a human embryo. Together, isCORAL enables lineage-resolved studies of development and disease from standard single cell and spatial transcriptomes, and provides an explicit representation of lineage memory for future virtual cell models.

systems biology↗

A hippocampal digital Twin reveals latent structure in freely flying bats

Concurrent advances in artificial intelligence (AI), large-scale neuronal recording, and behavioral tracking have enabled increasingly powerful predictive models of brain-behavior relationships. Yet predictive accuracy does not automatically yield interpretable principles of neural organization, particularly during natural behavior, where the relevant variables computed are often unknown in advance. Here, we developed a functional digital twin of the hippocampus, trained jointly on large-scale neural activity and self-directed three-dimensional flight in freely flying bats. A multimodal, multitask transformer accurately predicted both neural activity and behavior, outperformed standard approaches, and generalized across recording sessions. Interrogating the model's representations suggested a form of hippocampal generalization across self-selected trajectories that was not apparent in physical coordinates, but was plainly visible in the model's low-dimensional latent space. We confirmed this organization directly in the recorded neural activity: neurons fired at corresponding stages of spatially distinct paths connecting the same origin and destination, preserving their relative firing order even as their firing fields shifted with the path. Analysis of neuron-specific readouts further identified functional relationships among neurons that generalized from flight to waking rest and sleep, brain states never used for training, and differed systematically between the hippocampal subregions CA1 and CA3. Together, these results show how AI-based functional digital twins can complement conventional analysis by generating testable hypotheses about neural organization during natural behavior.

neuroscience↗

Terminal Modification Reprograms Supramolecular Organization of Integrin Ligand Assemblies to Shape Cell Migration

Precise organization of bioactive ligands at material-cell interfaces is critical for directing integrin-mediated cell behavior, yet tuning supramolecular organization commonly necessitates orchestrated redesign of molecular composition or ligand sequence. Here we establish terminal modification as a minimal, sequence-preserving strategy to reprogram the organization and function of self-assembling integrin ligands. Using FFFIKVAV as a model system, N- and C-terminal modifications generated distinct supramolecular states with markedly different integrin activation and cell migration responses. Notably, stronger intermolecular association did not produce stronger biological activity, as N-terminal acetylation promoted scaffold consolidation while reducing the configurational freedom of the exposed IKVAV ligand and diminishing integrin activation and cell migration. Alongside modulating migration magnitude, terminal chemistry also diversified the cellular programs supporting migration, with the parent peptide and its C-terminally amidated analogue favoring protrusion-dominant and stress-fiber-dominant adhesion-cytoskeletal programs, respectively. These functional states were reproduced when the assemblies were introduced directly to pre-adherent cells, extending their activity beyond preformed material coatings. Our findings identify terminal chemistry as a compact molecular design variable that links supramolecular organization to ligand function while diversifying the biological output of a shared bioactive sequence.

bioengineering↗

A self without a "we": Individuals with Borderline personality disorder show signatures of disrupted social basis functions

A capacity to navigate social relationships is fundamental to human wellbeing. However, the cognitive mechanisms underlying social dysfunction in psychiatric conditions remain poorly understood. Using an abstract multi-person decision making task that isolates the relational structure of multi-person interactions, we compare non-clinical controls (NCC, n=51) and individuals with BPD symptoms (n=46), a condition characterized by disturbances in self-other boundaries and chronic feelings of loneliness. Generally, we found a pattern of less self-centered decision-making in BPD. More specifically, individuals with BPD showed signatures of perceiving opponents as a coherent group ("them"), but a markedly reduced tendency to represent themselves as part of their own team ("us"). This pattern of results points towards a disruption of a primary social basis function. Our laboratory findings extend to experienced loneliness in daily life as measured by ecological momentary assessments (EMA). Together, this suggests that BPD is characterized by an unbalanced representation of social structure, with an attenuated "we" alongside a heightened "they".

neuroscience↗

An integrated platform for genome-wide functional analysis in Aspergillus niger through Ac/Ds insertion profiling and metabolic modeling

Genome-scale metabolic models guide rational strain engineering, while high-throughput insertional mutagenesis enables systematic investigation of gene function and condition-dependent growth requirements. However, a platform integrating high-density transposon insertion sequencing with matched stoichiometric, thermodynamic, enzyme-constrained and combined metabolic models has not, to our knowledge, been reported in Aspergillus. Here, we establish a unified experimental and computational platform in Aspergillus niger ATCC1015 by combining curated metabolic reconstruction, Ac/Ds transposon mutagenesis and machine-learning-based essentiality prediction. Our stoichiometric reconstruction, FBA1015, expands reaction coverage and compartmental resolution beyond four published reconstructions. From FBA1015, we developed three models sharing its biochemical network: GECKO light with enzyme-capacity constraints, TFA with thermodynamic constraints and ecTFA combining both. FBA1015 and its derivatives performed competitively in phenotype benchmarks, with added constraints improving agreement with measured growth and gas exchange. Insertion libraries grown in rich medium, glucose or xylose achieved genome-wide densities of one distinct site per 21--112bp across individual libraries. A machine-learning classifier integrated insertion patterns and gene structure to predict essentiality across 11,111 genes. Applying a stringent consensus criterion identified 709 genes predicted essential on both glucose and xylose as sole carbon sources, and 91 predicted essential on one but nonessential on the other. Integration with simulated gene deletions prioritizes candidate genes and testable pathway hypotheses, connecting high-throughput genetic screening with mechanistic analysis for fungal functional investigation and strain engineering.

microbiology↗

Direct electrochemical cortisol detection via transition-resolved interrogation at a defect-engineered graphene interface

Continuous tracking of cortisol is central to understanding human stress physiology, yet direct electrochemical detection without biological receptors remains challenging despite its promise for stable and dynamic sensing. Electrochemical reduction of cortisol typically occurs at highly negative potentials, where parasitic interfacial currents, hydrogen evolution, and substantial capacitive background overlap with the cortisol reduction signal, preventing accurate quantification. We overcome this barrier through an integrated material-measurement strategy combining a defect-engineered graphene interface with a transition-resolved interrogation (TRI) measurement strategy. First, we engineered polybenzimidazole-derived laser-induced graphene containing nitrogen-rich defects while suppressing oxygen-derived functionalities which reduced parasitic background currents within the same cathodic potential regime. Next, we designed TRI to leverage differences in the time-dependent evolution of overlapping cathodic processes to isolate a localized cortisol-associated electrochemical reduction transition. Derivative-domain projection coupled with background estimation enables its reliable quantification. This integrated sensing architecture enables sensitive, selective, and dynamic cortisol detection in both artificial and biological interstitial fluids at low nanomolar concentrations. The response remains reproducible across physiologically relevant variations in pH, ionic strength, temperature, and repeated cycling. Together, these capabilities provide a basis for continuous electrochemical cortisol monitoring for future study of stress physiology.

bioengineering↗

Sequence-to-function deep learning decodes human cis-regulatory evolution

Deciphering the regulatory consequences of sequence divergence across human evolution is essential to understanding the molecular basis of human-specific traits and disease. Although millions of derived alleles distinguish humans from great apes, only a small fraction are likely to influence human-specific traits. Previous studies have focused on regions of elevated sequence divergence, assuming that rapid evolution reflects functional adaptation, yet individual high-impact regulatory mutations evade such scans. Here, we apply sequence-to-function deep learning to predict chromatin accessibility across modern human, archaic hominin, and great ape personalized genomes, identifying lineage-specific cis-regulatory elements (linCREs) across diverse cellular contexts. Compared to conserved elements, linCREs are shorter, less pleiotropic, less conserved, and enriched in neurodevelopmental pathways. Many linCREs occur in regions with limited sequence divergence that acceleration-based approaches would overlook. We validate lineage-specific enhancer activity through luciferase reporter assays and demonstrate that a single motif-generating derived allele nominated by model interpretability tools drives a hominin-specific neurodevelopmental enhancer.

genomics↗

Transcription-specific synaptic plasticity mediates engram computations

Memory is encoded by sparse ensembles of neurons. While activity-dependent transcription and learning-induced synaptic plasticity are causally related to memory formation and recall, the link between the transcriptional regulation of synaptic plasticity and memory computations remains elusive. In particular, even though transcriptionally defined neuronal ensembles within a memory engram exhibit specific forms of synaptic plasticity and support distinct behavioral outputs, it is still unclear whether transcription-specific synaptic plasticity drives ensemble computations, rather than merely serving as a marker of ensemble identity. Here, we demonstrate that transcription-specific synaptic plasticity enables ensemble computations essential for learning-induced adaptive behaviors. In the mouse dentate gyrus (DG), we found that neuronal ensembles genetically defined by Fos-dependent transcription engage plasticity in feedforward excitatory synapses, whereas those defined by Npas4-dependent transcription engage plasticity in recurrent inhibitory synapses. We modeled spiking neural networks with transcription-specific synaptic plasticity and observed that Fos- and Npas4-dependent ensembles emerged following learning and stabilized with memory consolidation. Our computational model predicted that blocking Fos- or Npas4-dependent synaptic plasticity disrupts memory generalization and discrimination, respectively. By acutely deleting Fos or Npas4 in the DG to selectively block Fos- or Npas4-dependent synaptic plasticity, we conducted contextual fear conditioning experiments whose results supported our computational model's prediction. Our study provides causal evidence that specific transcriptional programs induced in distinct neuronal ensembles differentially engage synaptic plasticity and thereby regulate memory computations.

neuroscience↗

Extracellular vesicles drive cross-genus mycovirus transmission and suppress two fungal diseases

Mycoviruses are typically transmitted vertically through fungal reproduction or horizontally via hyphal anastomosis, but identical viruses in phylogenetically divergent fungi hint at unknown inter-species transmission mechanisms. Here, we identify fungal extracellular vesicles (EVs) as mediators of cross-genus mycovirus transmission. Using the hypovirulent Botrytis cinerea strain IBc-374 (harboring 16 mycoviruses) as a donor, we show that up to 13 mycoviruses are horizontally transmitted to Sclerotinia sclerotiorum during dual culture or plant co-inoculation, even though these two fungi belong to different genera and are generally considered incapable of hyphal anastomosis. Electron microscopy reveals abundant vesicle structures in IBc-374 hyphae, and nanoparticle tracking analysis showed that the strain secretes >11-fold more EVs than a virus-free strain. RT-PCR detects genomic RNAs of 7 mycoviruses in purified EVs, and the full-length viral genome in EVs was further validated with BcHV5 as example by fluorescence in situ hybridization and RT-PCR. Incubation of protoplast-derived germlings of S. sclerotiorum or B. cinerea with IBc-374 EVs leads to infection by 4-6 donor mycoviruses, demonstrating EV-mediated cross-genus transmission. Injection of mycovirus-carrying EVs into tobacco leaves followed by fungal inoculation also transmits two hypoviruses to both species. Application of IBc-374 hyphal fragment suspension significantly reduces lesion sizes caused by both pathogens on plants, and rescued two pathogens carrying multiple mycoviruses exhibit hypovirulence and impaired growth. Our findings reveal EVs as a cell-free vector that bypasses vegetative incompatibility, providing a mechanistic basis for cross-species viral spread and opening avenues for EV-based virus cocktails to control multiple fungal diseases. IN BRIEFWu et al. discover that fungal extracellular vesicles (EVs) can package and transmit multiple mycoviruses across genera from Botrytis cinerea to Sclerotinia sclerotiorum. EV-mediated delivery overcomes vegetative incompatibility barriers and reduces disease caused by both fungal pathogens, offering a cell-free strategy for mycovirus-based biological control.

microbiology↗

Microbial communities in tropical soils are highly resilient to fluctuating redox conditions

Many wet tropical soils alternate frequently between fully oxygenated and anaerobic conditions, constraining the terminal electron acceptors available for microbial metabolism, and the mineral-organic matter interactions that regulate many aspects of soil carbon (C) cycling. However, it is still unclear how fluctuating soil redox conditions influence the microbial community composition and if microbially mediated C flux is sensitive to extended oxic or anoxic periods like those observed during drought and flooding respectively. Using a 44-day redox manipulation of tropical soils that experience daily-to-weekly oxygen (O2) fluctuations in the field, we measured how different redox regimes shape soil biogeochemistry and microbial and metabolite composition. Replicate microcosms were exposed to four treatments (static oxic, static anoxic, high frequency fluctuation (4 day oxic/4 day anoxic), or low frequency fluctuation (8 day oxic/4 day anoxic)) regimes, and harvested for microbial, metabolite, carbon dioxide (CO2) flux, and biogeochemical assays at multiple timepoints. Oxic and fluctuating redox conditions caused the microbial community to shift in a manner correlated with soil iron content and directly orthogonal to communities from anoxic soils. The identity of both iron oxidizers and iron reducers was distinct in static anoxic soils but was resilient to redox fluctuation and prolonged O2 exposure. The total amount of CO2 respired was similar across all four redox regimes. Water-extractable organic matter composition was distinct across redox treatments, with anoxic soils accumulating higher levels of carbohydrate-, proteins-, amino sugar-, and lignin-like compounds consistent with reduced enzymatic decomposition and release of mineral-associated organic matter via iron reduction, while oxic soils showed elevated lipid- and unsaturated hydrocarbon-like compounds indicative of greater microbial biomass turnover. The microbial community adapted to dynamic redox conditions and the results substantiate cycling of distinct C compounds under varying redox conditions resulting from varying bioavailability (driven by mineral-OM dynamics) and/or shifted microbial metabolism.

microbiology↗

Screening of Isolation and Culture Conditions of Lactic Acid Bacteria in Mongolian Horse Feces

ObjectiveThis study aimed to establish an efficient isolation, culture, and preservation system for lactic acid bacteria from Mongolian horse feces by systematically evaluating the effects of sampling methods, culture conditions, media types, and cryopreservation protocols. MethodsFecal samples were collected using rectal and natural defecation methods, and bacteria were isolated by the spread plate technique, with isolates subcultured and identified via 16S rRNA gene sequencing. The performance of five commercial media (A-E), aerobic versus anaerobic conditions, and different glycerol concentrations (10% and 30%), temperatures (-20 {degrees}C and -80 {degrees}C), and storage durations (7, 15, and 30 days) were compared. ResultsRectal sampling showed significantly higher lactic acid bacterial survival and greater species diversity (12 vs. 8). Anaerobic culture yielded substantially higher counts and diversity (707 strains, 12 species) compared to aerobic conditions (36 strains, 5 species). Medium C (M.R.S. AGAR) exhibited the best isolation performance, producing the highest number of strains (311) and species (11), with selective enrichment for both bacilli and cocci. Glycerol effectively improved strain survival during sample cryopreservation, with the optimal short-term storage ([≤]15 days) achieved at -20 {degrees}C with 30% glycerol. Functional screening of randomly selected strains from optimized conditions demonstrated promising growth, acid and bile salt tolerance, and antimicrobial activity. ConclusionRectal sampling combined with anaerobic incubation using Medium C is recommended for optimal isolation. For samples that cannot be processed immediately, short-term preservation at -20 {degrees}C with 30% glycerol prior to isolation is effective. This study provides practical technical references for the acquisition and preservation of equine intestinal lactic acid bacteria resources.

microbiology↗

Integrative AI-Enabled Virtual Cell Modeling Reveals a Clinically Relevant Latent Effector State of Human CD8 T Cells Undetectable by Conventional Analyses

Understanding how immune checkpoint inhibitors (ICIs) reshape human T-cell responses requires models that move beyond static transcriptomic snapshots and discrete cell-state classifications. Here, we present an integrative AI-enabled virtual cell framework that represents human CD8 T-cell responses as dynamic and computable systems during ICI therapy. By integrating single-cell RNA sequencing with paired T-cell receptor sequencing within the C2S-scale foundation model, we construct a virtual representation of individual T cells, in which each cell is encoded by a unique functional identity that captures its transcriptional, signaling, and clonal characteristics. Using this framework, we identify a previously unrecognized dynamic latent effector state of CD8 T cells characterized by intermediate expression of effector genes, distinct signaling activity, and ongoing clonal expansion. Across independent patient cohorts, the virtual cell model consistently indicates that ICI therapy mainly acts by unmasking pre-existing effector potential rather than inducing de novo effector differentiation. Notably, this latent effector population remains transcriptionally restrained despite active signaling and clonal expansion, revealing a hidden reservoir of antitumor immune capacity. More broadly, our study demonstrates how AI-enabled virtual cell modeling can reconstruct latent cellular states and their dynamic transitions from multidimensional single-cell data. By incorporating functional identity into virtual cell model, this framework uncovers biologically meaningful yet non-obvious T-cell effector program during cancer immunotherapy and provides a generalizable approach for studying immune dynamics in human disease.

immunology↗

Pervasive historical introgression across oak phylogeny shapes gene expression

Oaks were once described as the "worst-case scenario" for the biological species concept because of the presumed pervasive hybridization and introgression among species. However, we still lack a full picture of genome-wide introgression across the eight sections of the Quercus phylogeny. Furthermore, we still do not have a complete characterization of what is introgressed and how it functionally influences the recipient species. Firstly, we used 168 whole genomes from 67 Quercus species belonging to the eight sections of the Quercus phylogeny and a super pan-genome to generate a phylogeny and test for ILS and introgression. Introgression was widespread: ancient introgression occurred between ancestors of the eight sections and more recent introgression took place within sections. Secondly, using genome-wide transcriptome, methylome, and chromatin accessibility data from a subset of 19 species sampled from four sections we demonstrated that introgressed genes are more highly and uniformly expressed than non-introgressed ones. This difference in expression level between introgressed and non-introgressed genes mostly results from cis-regulation, and is most likely due to DNA methylation decay in promoter ACRs. In summary, introgression has been a major evolutionary force during the whole evolutionary history of Quercus and had a significant impact on fundamental processes such as gene regulation and expression.

evolutionary biology↗

ProtSyntax: a protein large language model for decoding post-translational modification syntax and function

Post-translational modifications (PTMs) expand protein function by encoding context-dependent regulatory states, and their dysregulation contributes to cancer, neurodegeneration and metabolic disease. However, existing methods treat PTMs as independent residue labels, limiting their ability to distinguish contextually permissible sites, model crosstalk and infer functional consequences. Here we introduce ProtSyntax, a PTM-aware foundation protein language model combining protein-aware positional encoding, bidirectional state-space propagation, geometry-constrained attention and adaptive multi-objective learning. This design integrates residue chemistry, motif order, long-range context and three-dimensional microenvironments while coupling PTM recognition to enzyme function. Across 40 PTM-site benchmarks, ProtSyntax exceeded the strongest baselines in mean MCC and AP by 12.66% and 10.67%. ProtSyntax also recovered masked PTM types and sites, rejected structural decoys, generalized to data-scarce modifications, reconstructed crosstalk and linked PTM perturbations to enzyme kinetics. Applications to pathogenic variants, biomolecular condensates and disease-associated PTM landscapes demonstrate its potential to decode the regulatory language of the modified proteome.

bioinformatics↗

A novel AR molecular glue degrader via bivalent engagement of the N-terminal domain and RNF213-UBE2J2 complex

Targeted protein degradation enables the elimination of disease-relevant proteins through induced proximity between E3 ligases and substrates. Current androgen receptor (AR) therapies act via the ligand-binding domain (LBD) but fail against constitutively active LBD mutants or splice variants such as AR-V7. Here, we identify GZL626, a small-molecule degrader that induces proteasome-dependent degradation of both full-length AR and AR-V7. GZL626 suppresses AR transcriptional activity, inhibits proliferation of AR-positive prostate cancer cells, and blocks SARS-CoV-2 infection. Mechanistically, GZL626 binds the intrinsically disordered AR N-terminal domain (NTD) and promotes formation of a noncanonical RNF213-UBE2J2-AR ternary complex that drives AR ubiquitination and degradation. The AR DNA-binding domain (DBD) acts as a structural hub within this assembly. Distinct from PROTACs or classical molecular glues, GZL626 engages both AR and RNF213 bivalently, remodeling protein interactions to stabilize a functional E3-E2-substrate complex. These findings establish GZL626 as a first-in-class NTD degrader with potential to overcome resistance in advanced prostate cancer.

biophysics↗