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Biology subjects

Lin, C.-H.

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

At least 19 recordsLinked to original sources

Streptococcus pyogenes transforms the salivary proteome during controlled human infection

Streptococcus pyogenes (Group A Streptococcus, GAS) is among the leading causes of infectious mortality and primarily manifests as acute pharyngitis. The development of an effective vaccine continues to be hindered by an incomplete understanding of the host immune response, particularly in the oropharynx. Here, we provided detailed insights into the dynamic salivary proteome during acute illness in a human clinical trial of controlled infection of 20 healthy adults (CHIVAS-M75 trial). Deep profiling of salivary proteins via mass spectrometry revealed a striking increase in pro-inflammatory plasma proteins such as alpha1-antitrypsin and elements of the complement system during peak infection as a clear indication of the acute phase response in the oral environment. Many of these proteins, such as fibrinogen, are well-defined targets of key streptococcal virulence factors, with others, such as vitronectin, suggested to play a role in the host-pathogen relationship. Several salivary proteins with known antimicrobial properties, such as mucin-7 and cystatin, decreased universally across the infected cohort. For the first time, we have described the local and immediate protein response to acute pharyngitis in the oral cavity, highlighting a general host inflammatory signature and an abundance of GAS virulence targets infiltrating to the site of infection.

molecular biology↗

Immobilised enzyme reactors for post-production glycan modification of purified glycoproteins

Controlling protein glycosylation as a critical quality attribute of biopharmaceuticals remains challenging when glycosylation is coupled to cellular production systems. Here, we present a proof-of-concept glycosyltransferase immobilised enzyme reactor (IMER) housed within a 3D-printed column that enables directed post-production glycan modification of purified glycoproteins. Using {beta}-1,4-galactosyltransferase ({beta}4GalT1-IMER) and -2,6-sialyltransferase (ST6Gal1-IMER) immobilised on Ni-NTA resin, the IMER achieved near-complete galactosylation and substantial sialylation of partially deglycosylated bovine fetuin N-glycans with their respective substrates with a maximum substrate-enzyme contact time of four minutes. Isomeric-level analysis revealed arm-specific addition preferences for both enzymes, consistent with known specificities. The modular IMER design permits sequential connection of individual enzyme chambers, potentially offering a scalable, plug-and-play platform for constructing defined glycan structures on recombinant glycoprotein therapeutics.

molecular biology↗

Spatiotemporal secondary hair follicle development in the Lanyu pig (Sus scrofa taivanus): a novel pelage hair follicle model

Large full-thickness (LFT) skin wounds remain a major clinical challenge, and progress in regenerative medicine has been limited by poor translation from animal models to humans. A key limitation is that commonly used species such as mice, rats, and rabbits are loose-skinned, whereas humans are tight-skinned with distinct skin architecture. Although pigs more closely resemble human skin, widely used breeds have lost secondary (vellus-like) hair follicles through artificial selection, restricting their utility for studying ectodermal organ regeneration. Here, we characterize the development, patterning, and molecular features of secondary hair follicles in the Lanyu pig (Sus scrofa taivanus), an indigenous breed that retains these structures. Whole-mount and histological analyses revealed two distinct follicle populations: primary follicles arranged in stable triplet clusters and smaller secondary follicles distributed interstitially. A developmental time course using alkaline phosphatase (ALP) staining identified sequential stages of secondary follicle morphogenesis--placode, hair germ, hair peg, and mature follicle--occurring after primary follicle establishment. Immunohistochemical analysis demonstrated conserved epithelial- mesenchymal interactions, progressive epithelial stratification, and dynamic {beta}-catenin signaling during secondary follicle development. Keratin expression patterns and follicular architecture closely resembled those of human vellus hair follicles, supporting the translational relevance of this model. Notably, secondary follicles were retained into adulthood, and genetic analyses of outcrossed animals suggest that this trait follows an autosomal dominant inheritance pattern. Together, these findings establish the Lanyu pig as a tight-skinned mammalian model that preserves vellus-like hair follicles, providing a platform for investigating hair follicle-mediated skin regeneration and improving translational relevance for human wound healing.

developmental biology↗

Mitochondrial Transplantation in the Eye: A Review and Evaluation of Surgical Approaches

PurposeMitochondrial dysfunction contributes to major blinding diseases, including age-related macular degeneration and glaucoma. Although mitochondrial transplantation has shown therapeutic potential in multiple organ systems, translation to the eye remains limited, partly due to uncertainty regarding optimal delivery. We summarize the biologic rationale and preclinical evidence supporting ocular mitochondrial transplantation and present feasibility data evaluating clinically relevant delivery routes. MethodsWe conducted a focused narrative review of ocular mitochondrial transplantation. For feasibility experiments, mitochondria with an endogenous fluorescent dye were isolated from liver donor mice. Postnatal day 7 pups received subretinal injections, and adult CD1 mice received intravitreal injections, including optic nerve head directed delivery. Eyes were analyzed using fluorescence microscopy and immunohistochemistry. Mitochondrial uptake was assessed in cultured retinal pigmental epithelial (RPE) cells using co-incubation assays. Suprachoroidal delivery feasibility was evaluated in cadaveric human near-real surgical specimens using a novel dedicated suprachoroidal injector. ResultsThe literature on ocular mitochondrial transplantation remains limited and consists primarily of small preclinical studies using intravitreal delivery and imaging-based detection. In our experiments, intravitreal delivery produced donor signals predominantly within inner retinal layers, with enrichment along retinal nerve fiber bundles when directed toward the optic nerve head. Cultured RPE cells demonstrated dose-dependent uptake of exogenous mitochondria. Subretinal delivery localized donors signal to the RPE and adjacent outer retina. Suprachoroidal injections demonstrated procedural feasibility with reliable access to the suprachoroidal space and visible injectate distribution. ConclusionsOcular mitochondrial transplantation is in an early stage of investigation. Our feasibility data indicate that established posterior-segment delivery routes expose distinct retinal compartments and that route selection strongly influences anatomic distribution. Further studies are needed to verify intracellular uptake, define dosing and durability, and evaluate safety in disease-relevant models.

cell biology↗

The tumour suppressor RBM5 activates the helicase DHX15 to regulate splicing

Pre-mRNA splicing determines the expressed proteome and is frequently dysregulated in cancer. The tumour-suppressor RBM5 controls an exon network regulating apoptosis, yet its molecular mechanism is elusive. Using in vivo spliceosome capture and cryogenic electron microscopy, we determined structures of precatalytic spliceosomes arrested by RBM5 immediately after U2 snRNP branchpoint recognition. Despite intron diversity, the U2-pre-mRNA duplex, branchpoint adenine, and downstream polypyrimidine tract are well-resolved. RBM5 binds the outer SF3B1 HEAT surface and performs dual functions: First, its helix-loop-helix motif and upstream zinc-finger domain sterically block tri-snRNP and Prp8 docking and prevent progression to pre-B and Bact complexes; Second, its G-patch activates DHX15 and places this DExH-box helicase on the pre-mRNA as it exits SF3B1, poised for branch helix unwinding. DHX15 binding to SF3B1 is facilitated by U2SURP/SR140, which engages SF3B1 near RBM5s helix-loop-helix. Functional assays confirm that disruption of the RBM5 interfaces with either DHX15 or SF3B1 inhibit exon repression. Mutations at these regulatory interfaces are common in cancer genomes and predicted to disrupt its regulation of apoptotic isoforms. Thus, RBM5 acts as a dual-action spliceosome gatekeeper that couples helicase activation with physical stalling to enforce tumour-suppressive alternative splicing programmes.

molecular biology↗

Robust volumetric multiplex staining of centimeter-scale FFPE tissues guided by neural network-based optimization

Archived formalin-fixed, paraffin-embedded (FFPE) tissues, including brain-bank specimens, are valuable resources for disease research, but rapid cyclic immunolabeling of intact specimens remains challenging. Here, we present FIDELITY, an epoxy-free workflow that balances optical transparency, immunostaining performance, and tissue integrity for multi-cycle protein profiling in centimeter-thick FFPE specimens. Neural network-guided optimization identified an SDS-glycine formulation that integrates delipidation and epitope retrieval while preserving tissue stiffness, replacing prolonged epoxy reinforcement and subsequent high-temperature antigen retrieval with a single aqueous pretreatment. Application to human Alzheimer's disease specimens enabled volumetric imaging and quantitative analysis while retaining compatibility with conventional histopathology. Its compatibility with active electrophoretic staining further supported rapid labeling and five rounds of immunolabeling in a whole FFPE mouse brain. Two-round labeling of a human glioma specimen further demonstrated the applicability of the cyclic workflow to human pathological tissue. Together, FIDELITY provides a practical platform for large-volume, multiplexed protein profiling of intact FFPE specimens.

neuroscience↗

Dephosphorylation of YES kinase-mediated co-chaperone DNAJB6b phosphorylation attenuates tau protein aggregation

Alzheimers disease (AD) is a neurodegenerative disorder characterized by a gradual deterioration of memory. Here, we examine the biological consequences of phosphorylation-mediated chaperone activity in AD-associated tau aggregates. Increased phosphorylation of DNAJB6b at Y53 is observed in the brain lysates of AD patients. Our research found that an activated Src family kinase, YES, phosphorylates Y53 within the J-domain of DNAJB6b and enhances the binding between DNAJB6b and Hsp70. The strengthened association between DNAJB6b and Hsp70 may lead to the accumulation of tau aggregates. These findings suggest that the up-regulation of YES kinase modifies DNAJB6b, and that the resulting alteration of DNAJB6b-dependent tau disaggregation may contribute to an increased risk of developing AD. Additionally, phosphor-DNAJB6b at Y53 may serve as a biomarker for the prognosis and diagnosis of AD.

neuroscience↗

Exploration of American Elderberry Bioactive Compounds for Inhibition of the Influenza Virus Polymerase Acidic Endonuclease

Elderberries have been commonly used to relieve symptoms of influenza and the common cold. In this study, the antiviral activity of juices of American elderberry (Sambucus nigra subsp. canadensis) cultivars were evaluated against the recombinant N-terminal domain of Influenza A Polymerase Acidic protein using a Fluorescence Resonance Energy Transfer (FRET)-based endonuclease assay. The American elderberry cultivar Ozark showed the strongest inhibitory activity among 21 cultivars, followed by the wild accession 1196. The juice from four American elderberry cultivars Ozark, accession 1892, 1196, and 2084 demonstrated stronger inhibitory effect against nPA protein (>65% inhibition) compared to the European elderberry cultivar Haschberg, which showed 62% inhibition, suggesting a higher abundance of bioactive compounds in these cultivars, capable of interfering with Influenza PA activity. Among the elderberry compounds tested, gallic acid (IC50 11.56 {+/-} 1.80 {micro}M), myricetin (IC50 16.02 {+/-} 0.06 {micro}M), caffeic acid (IC50 22.75 {+/-} 0.9 {micro}M), and luteolin (IC50 27.92 {+/-} 0.72 {micro}M), showed the strongest inhibition of nPA endonuclease activity. These findings support the application of American elderberry in nutraceutical product formulations designed to help manage flu symptoms. To the best of our knowledge, this is the first study elucidating the anti-influenza mode of action of American elderberry against influenza molecular targets.

biochemistry↗

Quantification of bioactive compounds in the juices of 21 American elderberry cultivars

American elderberry (Sambucus nigra subsp. canadensis) is recognized as a rich source of bioactive compounds with nutritional and therapeutic potential. However, comprehensive quantification of its metabolites remains analytically challenging due to the structural complexity of phenolics and matrix interferences in juice extracts. In this study, a targeted ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) workflow was developed and validated to quantify 22 bioactive metabolites, including anthocyanins, flavonoids, and phenolic acids, in juices from 21 American elderberry cultivars. An optimized UHPLC- MS/MS system demonstrated higher sensitivity, selectivity, and throughput than conventional high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), achieving limits of detection and quantification below 0.1 ng/mL for most analytes. Matrix effects were effectively mitigated through sample dilution, enabling accurate and reproducible quantification across complex juice matrices. Quantification of metabolites showed that accession 1199 exhibited high levels of cyanidin-based anthocyanins, suggesting its utility as a natural food color source. Overall, high-throughput UHPLC-MS/MS method provides a robust analytical framework for metabolomic profiling for cultivar selection and the development of elderberry-derived functional products.

biochemistry↗

Distinct Flower signaling domains orchestrate cellular fitness via secreted vesicles in Aβ-induced neurodegeneration

Cellular fitness surveillance preserves tissue integrity, yet its regulation within the mammalian brain remains poorly understood. We identify a bifurcated mechanism in the transmembrane protein Flower--encoding both survival-promoting ("win") and apoptosis-inducing ("lose") isoforms. We demonstrate that astrocytes secrete specialized extracellular vesicles (EVs), termed "fitness vesicles," carrying Flower to facilitate competitive selection across distal cell populations. The N-terminal Flower domain acts extrinsically via these EVs to drive the elimination of less-fit neighbors. Conversely, the "win"-specific C-terminal domain functions as a cell-intrinsic module; it translocates to the nucleus under stress to repress Caspase-3 and provide resilience. In Alzheimers disease (AD) models and human AD brains, Flower-positive astrocytes accumulate around amyloid-{beta} (A{beta}) plaques. Under A{beta} stress, the "win" isoform reprograms astrocytes toward a neuroprotective state that enhances plaque clearance while ensuring cell-intrinsic survival. Our findings reveal how Flower couples long-range, EV-mediated cellular selection with cell-autonomous protection to coordinate astrocyte quality control and tissue resilience in neurodegeneration.

neuroscience↗

Impact of Long-Term Cover Cropped Organic Farming Practices on the Development of Disease Suppressive Soils

Numerous field studies have reported the disease-suppressive properties of the system in organic farming and cover crop practices. This research examined how long-term organic farming with cover-cropped systems enhance soil disease suppressiveness and changes the chemical composition of the rhizo-sphere related to disease resistance. The study proposed that the interactions between plant exudates and helpful microorganisms in these systems create conditions that are less favorable for harmful pathogenic organisms, resulting in soil that suppresses disease. To achieve the goals, we used an untargeted metabolomics approach to compare chemical profiles from long-term certified organic fields, including different cover crop termination methods like flail and rotary mowing, to conventionally managed plots. We analyzed rhizosphere soil extracts using ultra-high-pressure liquid chromatography combined with high-resolution mass spectrometry (UPLC-HRMS). We processed data with both MS-DIAL and XCMS, which included peak detection and feature grouping. We annotated metabolites using the MS-DIAL Public VS17 libraries for features derived from MS-DIAL and the METLIN database for features derived from XCMS. Our analysis identified over 2500 distinct soil compounds, showing that long-term cover cropping significantly changes the soils chemical environment. The treatments with cover crops showed a higher abundance and diversity of bioactive chemicals compared to the controls, and this enriched metabolic profile supported the formation of disease-suppressive soil.

plant biology↗

buzzdetect: an open-source deep learning tool for automated bioacoustic pollinator monitoring

Ecological studies of pollinators often require long-term and extensive monitoring, posing a significant cost and limitation to research. Traditional sampling methods of observation such as sweep netting and pan trapping provide valuable information on pollinator diversity, but scale poorly when conducting large sampling efforts across space and time. We introduce "buzzdetect", our tool to apply deep learning models to audio data for conducting passive acoustic monitoring on pollinators, and test our accompanying audio classification model. The model is capable of distinguishing the buzzing of insect flight from environmental noise with a sensitivity of 27% at a precision (true positive rate) of 95%. Application of buzzdetect to recordings made in pumpkin, watermelon, mustard, and soybean reveals differences in timing and intensity of foraging: foraging occurred the earliest in pumpkins and the latest for soybean while foraging activity was most intensive in mustard.

ecology↗

Lytic IFNγ is stored in granzyme B-containing cytotoxic granules and co-secreted by effector CD8⁺ T cells

Cytotoxic CD8 T cells form immunological synapses with target cells and release effector molecules, including IFN{gamma}, to mediate antitumor immunity. However, the mechanisms by which IFN{gamma} contributes to cytotoxicity remain incompletely understood. Here, we identify a subset of IFN{gamma} stored within GzmB cytotoxic granules (CGs) in activated mouse and human CD8 T cells, termed lytic IFN{gamma}. Lytic IFN{gamma} is polarized to the synapse and co-secreted with GzmB in both soluble and supramolecular attack particle (SMAP)-associated forms. Mouse CD8 T cells lacking the vesicle priming factor Munc13-4 exhibit impaired both CG and early IFN{gamma} release at the immunological synapse, while prolonged synaptic engagement restores IFN{gamma} secretion. Super-resolution imaging demonstrates that sustained synaptic interactions drive IFN{gamma} secretion at distal membrane sites, suggesting the existence of distinct IFN{gamma} populations with potentially diverse functions beyond lytic IFN{gamma}. These findings uncover an unrecognized mechanism of IFN{gamma} storage and release, underscoring its pivotal role in CD8 T cell-mediated tumor elimination.

immunology↗

Integrative multiomics analysis of metabolic dysregulation induced by occupational benzene exposure in mice

Background: Type 2 Diabetes Mellitus (T2DM) is a significant public health burden. Emerging evidence links volatile organic compounds (VOCs), such as benzene to endocrine disruption and metabolic dysfunction. However, the effects of chronic environmentally relevant VOC exposures on metabolic health are still emerging. Objective: Building on our previous findings that benzene exposure at smoking levels (50 ppm) induces metabolic impairments in male mice, we investigated the effects of occupationally relevant, below OSHA approved, benzene exposure on metabolic health. Methods: Adult male C57BL/6 mice were exposed to 0.9ppm benzene 8 hours a day for 9 weeks. We assessed measures of metabolic homeostasis and conducted RNA and proteome sequencing on insulin-sensitive organs (liver, skeletal muscle, adipose tissue). Results: This low-dose exposure caused significant metabolic disruptions, including hyperglycemia, hyperinsulinemia, and insulin resistance. Transcriptomic analysis of liver, skeletal muscle, and adipose tissue identified key changes in metabolic and immune pathways especially in liver. Proteomic analysis of the liver revealed mitochondrial dysfunction as a shared feature, with disruptions in oxidative phosphorylation, mitophagy, and immune activation. Comparative analysis with high-dose (50 ppm) exposure showed both conserved and dose-specific transcriptomic changes in liver, particularly in metabolic and immune responses. Conclusions: Our study is the first to comprehensively assess the impacts of occupational benzene exposure on metabolic health, highlighting mitochondrial dysfunction as a central mechanism and the dose-dependent molecular pathways in insulin-sensitive organs driving benzene-induced metabolic imbalance. Our data indicate that current OSHA occupational exposure limits for benzene are insufficient, as they could result in adverse metabolic health in exposed workers, particularly men, following chronic exposure.

pharmacology and toxicology↗

Cancer-associated SF3B1 mutation K700E causes widespread changes in U2/branchpoint recognition without altering splicing.

Myelodysplastic syndromes and other cancers are often associated with mutations in the U2 snRNP protein SF3B1. Common SF3B1 mutations, including K700E, disrupt SF3B1 interaction with the protein SUGP1 and induce aberrant activation of cryptic 3 splice sites (ss), presumably resulting from aberrant U2/branch site (BS) recognition by the mutant spliceosome. Here, we apply the new method of U2 IP-seq to profile BS binding across the transcriptome of K562 leukemia cells carrying the SF3B1 K700E mutation. For cryptic 3 ss activated by K700E, we identify their associated BSs and show that they are indeed shifted from the WT sites. Unexpectedly, we also identify thousands of additional changes in BS binding in the mutant cells that do not alter 3 ss choice. These new BS are usually very close to the natural sites, occur upstream or downstream, and either exhibit stronger base-pairing potential with U2 snRNA or are adjacent to stronger polypyrimidine tracts than the WT sites. The widespread imprecision in BS recognition induced by K700E with limited changes in 3 ss selection supports a positive role for SUGP1 in early BS choice and expands the physiological consequences of this oncogenic mutation.

molecular biology↗

Exploring American Elderberry Compounds for Antioxidant, Antiviral, and Antibacterial Properties Through High-Throughput Screening Assays Combined with Untargeted Metabolomics

American elderberry (Sambucus nigra subsp. canadensis) is a rapidly emerging new perennial crop for Missouri, recognized for its high level of bioactive compounds with significant health benefits, including antibacterial, antiviral, and antioxidant properties. A high-throughput screening assay combined with untargeted metabolomics analysis was utilized on American elderberry juice from 21 genotypes to explore and characterize these bioactive compounds. Our metabolomics study has identified 32 putative bioactive compounds in the American Elderberry juices. An array of high-throughput screening bioassays was conducted to evaluate 1) total antioxidant capacity, 2) activation of antioxidant response elements (ARE), 3) antiviral activity, and 4) antibacterial activity of the putatively identified compounds. Our results revealed that 14 of the 32 American elderberry compounds exhibited strong antioxidant activity. Four compounds (isorhamnetin 3-O-glucoside, kaempferol, quercetin, and naringenin) activated ARE activity and were found to be non-cytotoxic to cells. Notably, six of the 32 compounds demonstrated significant antiviral activity in an in vitro TZM-bl assay against two strains of HIV-1 virus, CXCR4-dependent NL4-3 virus and CCR5-dependent BaL virus. Luteolin showed the most potent anti-HIV activity against the NL4-3 virus (IC50 = 1.49 {micro}M), followed by isorhamnetin (IC50 = 1.67 {micro}M). The most potent anti-HIV compound against the BaL virus was myricetin (IC50 = 1.14 {micro}M), followed by luteolin (IC50 = 4.38 {micro}M). Additionally, six compounds were found to have antibacterial activity against gram-positive bacteria S. aureus, with cyanidin 3-O-rutinoside having the most potent antibacterial activity in vitro (IC50 = 2.9 {micro}M), followed by cyanidin 3-O-glucoside (IC50 = 3.7 {micro}M). These findings support and validate the potential health benefits of compounds found in American elderberry juices and highlight their potential for use in dietary supplements as well as innovative applications in health and medicine.

biochemistry↗

The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multi-part RNA regulatory modules

The Rbfox proteins regulate alternative pre-mRNA splicing by binding to the RNA element GCAUG. In the nucleus, most of Rbfox is bound to LASR, a complex of RNA-binding proteins that recognize additional RNA motifs. However, it remains unclear how the different subunits of the Rbfox/LASR complex act together to bind RNA and regulate splicing. We used a nuclease-protection assay to map the transcriptome-wide footprints of Rbfox1/LASR on nascent cellular RNA. In addition to GCAUG, Rbfox1/LASR binds RNA containing motifs for LASR subunits hnRNPs M, H/F, C, and Matrin3. These elements are often arranged in tandem, forming multi-part modules of RNA motifs. To distinguish contact sites of Rbfox1 from the LASR subunits, we analyzed a mutant Rbfox1(F125A) that has lost RNA binding but remains associated with LASR. Rbfox1(F125A)/LASR complexes no longer interact with GCAUG but retain binding to RNA elements for LASR. Splicing analyses reveal that in addition to activating exons through adjacent GCAUG elements, Rbfox can also stimulate exons near binding sites for LASR subunits. Mini-gene experiments demonstrate that these diverse elements produce a combined regulatory effect on a target exon. These findings illuminate how a complex of RNA-binding proteins can decode combinatorial splicing regulatory signals by recognizing groups of tandem RNA elements.

molecular biology↗

Neuronal lysosome transfer to oligodendrocyte precursor cells: a novel mechanism of neuron-glia communication and its role in neurodegenerative disease

Oligodendrocyte precursor cells (OPCs) shape brain function through intricate regulatory mechanisms. Here, we observed that OPC processes establish connections with neuronal somata, with smaller lysosomes positioned near these contact sites. Tracking lysosomes demonstrated neuronal lysosomes were attracted to and released at these contact points, eventually becoming incorporated into OPC processes, suggesting a selective, OPC-evoked release of lysosomes from neuronal soma and their ingestion by OPCs, highlighting a unique lysosome-mediated communication between neurons and OPCs. Diminished branching of OPC processes resulted in fewer neuron-OPC contacts, fostering larger lysosome accumulation in neurons, altered neuronal activity and escalated prevalence of senescent neurons during aging. A similar reduction in OPC branching and neuronal lysosome accumulation was evident in an early-stage Alzheimers disease mouse model. Together, these findings underscore the pivotal role of OPC processes in modulating neuronal activity through direct somatic contact and lysosome ingestion, presenting a prospective therapeutic avenue for addressing neurodegenerative diseases.

neuroscience↗