Biology subjects

Lin, H.

Publications and source records attributed to Lin, H..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Alcohol Disrupts Neural Differentiation Through Endoplasmic Reticulum Stress and PERK Pathway Activation

Prenatal alcohol exposure (PAE) can lead to fetal alcohol spectrum disorder (FASD), a condition marked by developmental brain defects that result in neurobehavioral and cognitive impairments. However, the underlying molecular mechanisms remain poorly understood. Brain development is a highly regulated process, with neurogenesis playing a crucial role. A key stage in this process is neural differentiation, which is essential for proper brain function. This study aims to investigate how alcohol disrupts neural differentiation. NE-4C cells, a neural stem cell line derived from the mouse embryonic brain, were utilized as an in vitro model. As an in vivo model, pregnant mice were exposed to alcohol between gestation days 14 and 16, after which newly formed neurons in the ventricular zone (VZ) were analyzed. To examine the role of endoplasmic reticulum (ER) stress, tunicamycin (TM), and MANF-deficient NE-4C cells were employed. Neural differentiation was assessed using immunofluorescence, immunoblotting and flow cytometry. Alcohol impaired the differentiation of NE-4C cells into neurons and astrocytes without impacting cell migration. It also induced ER stress, preferably activating the PERK pathway. Similarly, ER stress caused by TM and MANF deficiency disrupted neural differentiation and activated PERK. Inhibiting PERK mitigated alcohol-induced impairment of neuronal differentiation. PAE decreased the number of newly formed neurons in the VZ of fetal brain while having little effects on cell survival and proliferation. Inhibiting PERK partially reversed the reduction of new neurons caused by PAE. Thus, alcohol-induced ER stress, particularly PERK activation, may contribute to impaired neurogenesis linked to FASD.

pharmacology and toxicology↗

bioRxiv2025

Neural sampling from cognitive maps supportsgoal-directed planning and imagination

AI systems are becoming more intelligent, but at a very high cost in terms of energy consumption and training requirements. In contrast, our brains only require 20W of energy, they learn online, and they can instantly adjust to changing contingencies. This begs the question what data structures, algorithms, and learning methods enable brains to achieve that, and whether these can be ported into artificial devices. We are addressing this question for a core feature of intelligence: The capacity to plan and solve problems, including new problems that involve states which were never encountered before. We examine three tools that brains are likely to employ for achieving that: Cognitive maps, stochastic computing, and compositional coding. We integrate these tools into a transparent neural network model, and demonstrate its power for flexible planning and problem solving. Importantly, this approach is suitable for implementation by in-memory computing and other energy-efficient neuromorphic hardware. In particular, it only requires self-supervised local synaptic plasticity that is suited for on-chip learning. Hence a core feature of brain intelligence, the capacity to generate solutions to problems that were never encountered before, does not require deep neural networks or large language models, and can be implemented in energy-efficient edge devices.

neuroscience↗

bioRxiv2025

Environmental stress sensitivity determines bacterial Mn(II) oxidation

Bacterial Mn(II) oxidation is a widespread and ecologically significant process, with Mn oxides playing essential roles in biogeochemical cycling and environmental remediation. However, the environmental cues that initiate this microbial activity remain enigmatic. In this study, a spontaneous mutant was isolated from the previously characterized Arthrobacter strain that exhibited autonomous Mn(II)-oxidizing capacity, in contrast to the parental strain, which required cocultivation with other bacteria to initiate Mn(II) oxidation1. Comparative transcriptomic analysis suggested that a gene system encoding an environmental stress-sensing receptor controlled the transcription of boxA, a Mn(II)-oxidizing gene. These findings indicate that two conditions are required for bacterial Mn(II) oxidation: the presence of a Mn(II)-oxidizing gene and an environmentally responsive regulatory system capable of activating its expression. Based on this knowledge, eight additional bacterial strains were isolated that triggered Arthrobacter Mn(II) oxidation. Transcriptomic profiling revealed a robust positive correlation between boxA expression and genes encoding two-component signal transduction systems. Given their widespread distribution (approximately 23% of environmental bacterial genomes harbor Mn(II)-oxidizing gene homologs2) and constant exposure to diverse biotic and abiotic stressors, these bacteria are likely to undergo frequent Mn(II) oxidation triggered by microbial interactions or chemical signals. This study provides critical mechanistic insight into the environmental regulation of bacterial Mn(II) oxidation, addressing a longstanding gap in understanding its natural occurrence.

microbiology↗

bioRxiv2025

Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance

A subset of commensal bacterial strains secrete bacteriocins, such as lantibiotics, to establish and protect their niche in the gut. Because the antimicrobial spectrum of lantibiotics includes opportunistic pathogens, such as vancomycin-resistant Enterococcus faecium (VRE), they may provide an approach to reduce antibiotic-resistant infections. The impact of lantibiotic-producing bacteria on the complex microbial populations constituting the microbiome, however, remains poorly defined. We find that genes encoding lanthipeptides, including lantibiotics, are commonly present in the microbiomes of healthy humans and in dysbiotic microbiomes of hospitalized patients. In fecal samples collected from hospitalized patients, bacterial species encoding lantibiotic genes are present in greater abundance than lantibiotic-deficient strains of the same species. We demonstrate that the lantibiotic-producing bacterium, Blautia pseudococcoides SCSK, prevents intestinal recolonization of mice by a wide range of commensal species following antibiotic-induced dysbiosis and markedly reduces fecal concentrations of microbiota-derived metabolites associated with mucosal immune defenses. Lantibiotic-mediated dysbiosis results in sustained loss of colonization resistance against Klebsiella pneumoniae and Clostrioides difficile infection. Our findings reveal the potential impact of lantibiotic-producing bacterial species on microbiome resilience and susceptibility to infection following antibiotic treatment.

microbiology↗

bioRxiv2025

Forest biogeochemical monitoring indicates altered microbial communities, macronutrient availability, CO2 emissions and litter chemistry in root zone soil of oak trees with Acute Decline symptoms

Acute and Chronic Oak Decline (AOD & COD) widely impact oak woodlands across Europe. AOD is known to cause rapid decline in tree health in a short span of 3-5 years. However, the interactions between such oak decline and soil biogeochemical dynamics are not fully understood. We selected three oak trees for each of the three treatments for biogeochemical monitoring: 1. No symptoms (Healthy), 2. AOD & 3. COD symptoms, in Writtle woodlands, Essex, UK. The selected trees were used for quarterly root zone soil sampling (cores to depth of 40 cm), and monthly surface soil (0-10 cm), leaf litter and GHG emissions sampling over a year (2022-23). Soil samples were characterised for their physico-chemical properties, total nutrient content & availability. Leaf litter samples were sorted into branches, leaves, seeds and flowers, weighed and their chemistry characterised. Soil microbial communities were characterised using phospholipid fatty acid analyses. Almost all the measured properties showed significant changes with season and depth, indicating a strong temporal and depth effect on forest soil biogeochemical dynamics. Notably macro-nutrient contents of leaf litter were greater in the summer period, which resulted in increased soil nutrient availability in autumn. This pattern was particularly exaggerated in AOD trees, which had greater nutrient content in litterfall in summer and greater nutrient availability in root zone soil in autumn than those of COD and Healthy trees. We found that AOD root zone soil have altered microbial communities, decreased CO2 emissions and increased macronutrient availability. Taken together, our study shows poor physiological nutrient management by diseased AOD trees revealed by greater nutrient concentration in AOD leaf litter indicating the lack of nutrient resorption and re-allocation before leaf senescence, and less active root zone soil under AOD trees, shown by reduced soil CO2 emissions and increased nutrient availability in oak root influenced zones. Hence, we conclude that the biogeochemical dynamics of AOD root zone soils are significantly different to that of healthy and COD trees, however controlled experiments are needed alongside these field observations to disentangle the causes from effects in understanding the relationship between soil health and oak decline. HighlightsO_LIWe monitored forest soil biogeochemical dynamics under oak trees of different health status C_LIO_LIAcute Oak Decline (AOD) trees had greater macronutrient availability in root zone soils C_LIO_LIAOD trees had greater nutrient content in litter added to the root zone soil C_LIO_LIAOD root zone soils had altered microbial community structure & reduced CO2 emissions C_LIO_LIWe conclude that AOD trees have poor physiological nutrient management and less active rhizosphere compared to healthy trees. C_LI

ecology↗

bioRxiv2025

Tanycyte Bmal1 sex-specifically regulates weight gain and hypothalamic neurogenesis in female mice

The hypothalamic radial-glia-like tanycyte population plays important and intertwined roles in feeding and metabolism, reproduction, and seasonality. Although these processes are circadian-regulated and clock genes reportedly show robust cycling along the 3rd ventricle, the role of the clock in tanycytes has not yet been examined. We report here that clock genes cycle with much higher amplitude in ventral tanycytes compared to more dorsal ependymocytes of the 3rd ventricle, and that specific disruption of the tanycyte clock can be achieved by adult Bmal1 deletion using the RaxCreER driver. Adult tanycyte Bmal1 deletion did not affect circadian rhythms of wheel-running and sleep, but did inhibit weight gain on high-fat diet in female mice. Altered tanycyte-derived hypothalamic neurogenesis, which can regulate feeding and weight gain by contributing new neurons to nearby feeding-relevant nuclei, is one mechanism that likely contributes to this phenotype. Fate mapping studies showed that female mice have higher baseline tanycyte-derived neurogenesis than males, with many of the resulting neurons localizing to the feeding-relevant arcuate nucleus. Female but not male mice show reduced tanycyte-derived arcuate neurogenesis after adult tanycyte Bmal1 deletion and an increased percentage of newborn arcuate neurons take on a feeding-suppressing POMC neuropeptidergic fate. Thereby, skewing of feeding and satiety promoting fates link the weight homeostasis and neurogenesis effects. Together, our data establish tanycyte Bmal1 as a sexually dimorphic regulator of weight homeostasis, likely mediated at least in part by a female-specific neurogenesis effect in the feeding circuitry.

neuroscience↗

bioRxiv2025

Variational Autoencoders for Metabolomics: Data Imputation, Deconfounding, and Correlation Discovery

This protocol describes a computational approach for constructing correlation-based molecular networks from untargeted metabolomics data using MetVAE, a variational autoencoder-based framework. Complementing spectral similarity networks, it captures functional relationships re-flected in cross-sample correlations. The workflow imports metabolomics features and sample metadata, adjusts for compositionality, missingness, confounding, and high-dimensionality, esti-mates sparse metabolite correlations, and exports GraphML files for network visualization. In a hepatocellular carcinoma mouse model, it links lipid classes in high-fat-diet animals, suggesting an endogenous "auto-brewery" route to lipotoxic metabolites.

bioinformatics↗

bioRxiv2025

Gut Microbiota Dysbiosis and Short-chain Fatty Acid alterations in Pediatric New-Onset Type 1 diabetes with Ketoacidosis

ObjectiveDiabetic ketoacidosis (DKA) stands as the most common acute hyperglycaemic complication with a relatively high mortality rate among children diagnosed with type 1 diabetes (T1D). Previous studies have shed light on gut dysbiosis in newly-onset T1D children, but research targeting the gut microbiota and microbial metabolites in patients with DKA remains scarce. MethodsShotgun metagenomic analysis was conducted on fecal samples from 96 newly diagnosed T1D children, including 32 patients who presented with DKA upon admission. Short-chain fatty acids (SCFAs) were quantified using gas chromatography/mass spectrometry (GC/MS). Comparative analyses were performed on the gut microbiome and SCFA levels between DKA and non-DKA subgroups. ResultsGut microbiota composition differed between DKA and non-DKA groups. While alpha-diversity remained consistent, beta-diversity showed marked differences between the two groups, and the phyla Firmicutes and Bacteroidetes exhibited predominance in the DKA group. DKA was associated with increased potential pathogens and a significant depletion of SCFA-producing genera (Anaerobutyricum, Dialister, Ruminococcus, Roseburia, Dorea, and Butyricicoccus), accompanied by reduced SCFA levels. Further correlation analysis revealed strong associations between SCFAs, SCFA-producing microbiota, and disease severity indicators. Propionic acid and butyric acid mediated the association between SCFA-producing bacteria and DKA. ConclusionThis study first reported reductions in SCFAs and SCFA-producing bacteria in the fecal samples of T1D children at DKA onset. Our findings highlight SCFAs and their producers as protective biomarkers of DKA and suggest that targeting gut microbiota and SCFA metabolism may offer a potential therapeutic strategy for DKA. ImportanceWhile gut microbiota imbalances have been linked to type 1 diabetes (T1D), little is known about the role of gut microbes and their metabolites during acute diabetic ketoacidosis (DKA), an acute and life-threatening complication. This study examined the gut microbiome and levels of short-chain fatty acids (SCFAs) in fecal samples from children with new-onset T1D with and without DKA. DKA was characterized by distinct microbial signatures, including increased potential pathogens, a loss of beneficial SCFA-producing bacteria, and consistently lower SCFA levels. These changes closely correlated with indicators of disease severity, and further mediation analysis revealed the role of SCFAs in linking gut microbiota to DKA. These findings suggest that SCFAs and their producers may serve as protective markers for DKA, highlighting the potential of microbiome-based interventions to improve outcomes in children facing this critical complication.

microbiology↗

bioRxiv2025

Cryo-EM structure revealed a novel F-actin binding motif in a Legionella pneumophila lysine fatty-acyltransferase

Legionella pneumophila is an opportunistic bacterial pathogen that causes Legionnaires disease. To establish an intracellular niche conducive to replication, L. pneumophila translocates a diverse array of effector proteins that manipulate various host cellular processes, including the actin cytoskeleton. In a screen for effectors that alter actin dynamics, we identified a Legionella effector, Lfat1 (lpg1387), which colocalizes with the actin cytoskeleton in eukaryotic cells. Lfat1 specifically binds F-actin through a novel actin-binding domain (ABD). High-resolution cryo-electron microscopy (cryoEM) analysis revealed that this ABD forms a long -helix hairpin, with its tip interacting with subdomains I and II of two adjacent actin molecules within the F-actin filament. Interestingly, while individual -helices of the hairpin fail to bind F-actin, co-expression as separate fusion proteins restores binding activity. Furthermore, we demonstrated that Lfat1 exhibits lysine fatty-acyltransferase (KFAT) activity, targeting host small GTPases. These findings establish a foundation for studying the KFAT family of bacterial toxins and uncover a novel F-actin binding motif, providing an alternative F-actin marker with notable flexibility.

biochemistry↗

bioRxiv2025

CanASM: A comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer

Allele-specific DNA methylation (ASM) provides critical insights into the complex genetic and epigenetic mechanisms regulating gene transcription. Emerging evidence suggests that ASM is particularly enriched in gene enhancer regions, and recent studies have demonstrated that ASM is increased in cancer tissues compared with normal tissues. Despite the increasing recognition of ASM as a potential biomarker in tumorigenesis, systematic resources dedicated to identifying and annotating ASMs in cancer contexts remain limited. In this study, we developed CanASM (https://bioinfor.nefu.edu.cn/CanASM/), the first comprehensive database specifically designed to identify and annotate ASM in cancer. In CanASM, ASM sites identified from bisulfite sequencing data across 31 cancer types and their matched normal tissue samples are cataloged. Importantly, CanASM includes extensive regulatory annotations for ASMs, including associated genes, cis-regulatory elements and transcription factor binding colocalizations, transcription factor affinity changes, etc. Users can query and explore ASMs using various parameters, such as single-nucleotide variations (SNVs), chromosomal coordinates, and gene names. The current version of CanASM includes 5,003,877 unique SNV-CpG pairs, including 3,056,776 index SNVs, of which 2,634,406 are single-nucleotide polymorphisms (SNPs), and 4,157,508 CpGs. With an intuitive interface for browsing, querying, analyzing, and downloading, CanASM serves as a valuable resource for researchers investigating cancer-associated genetic variations and epigenetic regulation in cancer. Author summaryIdentifying target genes and regulatory mechanisms of cancer-associated genetic variants remains a major challenge in the post-GWAS era. Existing databases like Pancan-meQTL and ASMdb have contributed to uncovering the role of genetic variants in cancer by linking DNA variations to methylation. However, they lack comprehensive regulatory annotations for such sites and rely solely on genomic proximity for target gene prediction, overlooking distal interactions. Our analysis using 3D interaction data reveals that over 94.8% of ASMs exhibit distal regulatory relationships, emphasizing their critical role in cancer epigenetics. Furthermore, these databases cover a limited number of cancer types (Pancan-meQTL: 23, ASMdb: 8). To address these limitations, we developed CanASM, a database that provides ASMs identified from BS-seq data for 31 human cancers, along with multidimensional regulatory annotations for ASM sites. This includes target genes, cis-regulatory elements (enhancers, ATAC-seq regions, insulators, 3D interactions, CpG islands), TFBSs, and GWAS cancer trait associations. Additionally, CanASM offers three interactive tools for analyzing TF binding affinity changes, predicting ASM target genes through 3D interactions, and identifying cell marker variations. As a comprehensive resource for SNV-driven epigenetic regulation in cancer, CanASM is helpful for in-depth research in cancer genetics and epigenetics.

bioinformatics↗

bioRxiv2025

The multiomics landscape of small peptides encoded by long non-coding RNA-derived sORFs in rice

Long non-coding RNAs (lncRNAs), representing the non-coding RNA regions, constitute a significant portion of the genomes in complex organisms. Recent studies suggest that some lncRNAs have the capability to encode peptides. However, the presence of the lncRNA-derived sORFs-encoded polypeotides (LSEPs) in plants is not well understood. In this study, we developed a multi-omics approach that encompasses transcriptomics, translatomics (Ribo-seq), and proteomics to identify of LSEPs in rice. Among the 2764 identified lncRNAs, 42.69% were found to be bound by the ribosome, indicating a potential for encoding. Optimized small peptide extraction protocol was further developed, and the small peptides from rice leaves were extracted and subjected to LC-MS/MS analysis, leading to the identification of a total of 403 LSEPs across four constructed search databases. This work confirms the peptide-coding ability of lncRNAs in plants. Collectively, our study establishes an efficient multi-omics method for identifiying small peptides encoded by lncRNAs, which may be valuable for large-scare screening of LSEPs in plants.

plant biology↗

bioRxiv2025

Sirtuin 2 controls global protein synthesis by regulating Rheb-GTPase

Upregulated global protein synthesis is associated with the development and progression of several diseases and disorders. Strategies like calorie restriction and pharmacological inhibition of protein synthesis, have exhibited health-promoting effects. However, the complex molecular events that regulate global protein synthesis are not completely understood. Here, we report that SIRT2, a histone deacylase, negatively regulates global protein synthesis by inhibiting the mTORC1 pathway via deacetylating Rheb and promoting Rheb degradation. Our in vitro results suggest that SIRT2 deficiency increases protein synthesis, whereas SIRT2 overexpression suppresses protein synthesis. SIRT2-deficient mice exhibit age-associated and neurohormone-induced cardiac hypertrophy. Here, we report increased global protein synthesis in the hearts of young SIRT2-deficient mice, which may contribute to the development of cardiac hypertrophy. Conversely, cardiac-specific overexpression of SIRT2 reduces global protein synthesis in mice hearts. Mechanistically, SIRT2 binds to and deacetylates Rheb at K151 residue to enhance ubiquitin-proteosome-mediated degradation of Rheb. Depletion of Rheb rescues the increased protein synthesis in SIRT2-inhibited conditions. Our findings suggest that SIRT2 activation can be a potential therapeutic for treating diseases associated with increased protein synthesis.

cell biology↗

bioRxiv2025

SIRT2 Mediates Integrated Stress Response by Deacetylating and Stabilizing 4EBP1 to Suppress Translation

The ability to alleviate nutrient stress, such as amino acid limitation, is crucial for cell survival. The mTORC1 complex and integrated stress response (ISR) are mechanisms that sense the availability of amino acids and regulate ribosomal protein synthesis. Here we have discovered a new SIRT2-mediated pathway, downstream of ISR, that senses the limitation of amino acids to regulate translation. Under amino acid deprivation, SIRT2 protein level is upregulated translationally by its upstream open reading frame (uORF). SIRT2 in turn suppresses global protein translation, which helps cells to survive amino acid limitation. Mechanistically, we identified eukaryotic translation initiation factor 4E (eIF4E) binding protein 1 (4EBP1), which negatively regulates translation, as a substrate of SIRT2. SIRT2 deacetylates 4EBP1 at Lys69 and stabilizes 4EBP1 by protecting it from proteasomal degradation. Our study reveals a novel role for SIRT2 in regulating protein translation and a new regulatory mechanism of 4EBP1 in cells. Our study provides a better understanding of the intricate regulation of translation and may explain the known non-oncogene addiction role of SIRT2 in cancer cells.

cell biology↗

bioRxiv2025

In Situ Detection of α-Synuclein Seeding Activity Using Quiescent Seed Amplification Assay

The prion-like propagation of proteopathic -synuclein (Syn) "seeds" is a central pathogenic mechanism in synucleinopathies. However, methods to directly visualize this "seeding activity" within intact tissue are lacking. Conventional antibody-based techniques provide only static snapshots of pathological deposits, while sensitive seed amplification assays lose spatial information via mechanical fragmentation. Here, we introduce the Syn Quiescent Seed Amplification Assay (QSAA), a method for specific, robust, in situ amplification of Syn seeds directly within tissue sections. QSAA demonstrates superior sensitivity and earlier detection than pS129 and ThS staining, revealing widespread seeding in a PD mouse model, and successfully identifies endogenous seeds in archival human brains. By integrating with immunofluorescence, IF-QSAA uncovered microglial seeding activity and established that pS129 phosphorylation and seeding activity represent distinct pathological states. This offers unprecedented spatial insights into synucleinopathy pathogenesis, holding significant promises for early diagnosis and therapeutic evaluation.

neuroscience↗

bioRxiv2025

Aging-associated Increase of GATA4 levels in Articular Cartilage is Linked to Impaired Regenerative Capacity of Chondrocytes and Osteoarthritis

Although the causal association between aging and osteoarthritis (OA) has been documented, our understanding of the underlying mechanism remains incomplete. To define the regulatory molecules governing chondrocyte aging, we performed transcriptomic analysis of young and old human chondrocytes from healthy donors. The data predicted that GATA binding protein 4 (GATA4) may play a key role in mediating the difference between young and old chondrocytes. Results from immunostaining and western blot showed significantly higher GATA4 levels in old human or mouse chondrocytes when compared to young cells. Moreover, overexpressing GATA4 in young chondrocytes remarkably reduced their cartilage-forming capacity in vitro and induced the upregulation of proinflammatory cytokines. Conversely, suppressing GATA4 expression in old chondrocytes, through either siRNA or a small-molecule inhibitor NSC140905, increased the production of aggrecan and collagen type II, and also decreased levels of matrix-degrading enzymes. In OA mice induced by surgical destabilization of the medial meniscus, intraarticular injection of lentiviral vectors carrying mouse Gata4 resulted in a higher OA severity, synovial inflammation, and pain level when compared to control vectors. Mechanistically, we found that overexpressing GATA4 significantly increased the phosphorylation of SMAD1/5. Our work demonstrates that the aging-associated increase of GATA4 in chondrocytes plays a vital role in OA progression, which may also serve as a target to reduce osteoarthritis in the older population.

cell biology↗

bioRxiv2025

HighPlay：Cyclic Peptide Sequence Design Based on Reinforcement Learning and Protein Structure Prediction

The structural diversity and good biocompatibility of cyclic peptides has led to their emergence as potential therapeutic agents. Traditional cyclic peptide design relies on natural template modification and combinatorial chemical library screening, but suffers from bottlenecks such as limited molecular diversity, high cost, and time-consuming.AI technologies have improved design efficiency by predicting target binding patterns and generating scaffold structures, but they still require extensive laboratory screening. In this study, we propose HighPlay, which integrates reinforcement learning (Monte Carlo Tree Search) with the HighFold structure prediction model to design cyclic peptide sequences for protein targets, dynamically exploring the sequence space without the need of predefined target information. The model was applied to the design of cyclic peptide sequences for three different targets, which were screened and verified by molecular dynamics simulation, and showed good binding affinity. Specifically, the cyclic peptide sequences designed for TEAD4 target showed micromolar-level affinity in further experimental validation.

bioinformatics↗

bioRxiv2025

Effects of alcohol on gut microbiome in adolescent and adult MMTV-Wnt1 mice

Breast cancer is the most commonly diagnosed cancer in women worldwide, with alcohol consumption recognized as a significant risk factor. While epidemiological studies consistently show a positive correlation between alcohol consumption and increased breast cancer risk, the underlying mechanisms remain unclear. Recent evidence suggests that the gut microbiome--the diverse collection of microorganisms, including bacteria, viruses, and fungi, residing in the gastrointestinal tract--plays a pivotal role in systemic health and disease. This is achieved through its regulation of key physiological processes such as metabolism, immune function, and inflammatory responses. Disruption of the gut microbiome (dysbiosis) has recently been implicated in the development of breast cancer. We hypothesized that alcohol exposure induces gut dysbiosis, which in turn drives systemic inflammation and carcinogenic processes. Previously, we demonstrated that alcohol exposure promotes mammary tumor growth and aggressiveness in MMTV-Wnt1 (Wnt1) transgenic mice, an established model for investigating mechanisms of alcohol-induced tumor promotion. In this study, we sought to determine whether alcohol exposure induces gut dysbiosis in adolescent and adult Wnt1 transgenic mice and their wild-type FVB counterparts. Our findings revealed that alcohol exposure significantly reduced microbiome richness in adult Wnt1 and FVB mice. Alcohol exposure also markedly altered microbiome composition in adolescents and adults in both strains. Additionally, we identified specific microbial taxa that were significantly affected by alcohol exposure. These results demonstrate that alcohol disrupts the gut microbiome in a preclinical breast cancer model, providing insights into the potential role of gut dysbiosis in alcohol-induced mammary tumor promotion and offering avenues for future research.

cancer biology↗

bioRxiv2025

Super-resolving particle diffusion heterogeneity in porous hydrogels via high-speed 3D active-feedback single-particle tracking microscopy

Nanoparticle diffusion in 3D porous structures is critical to understanding natural and synthetic systems but remains underexplored due to limitations in traditional microscopy methods. Here, we use 3D Single-Molecule Active-feedback Real-time Tracking (3D-SMART) microscopy to resolve nanoparticle dynamics in agarose gels with unprecedented spatiotemporal resolution. We highlight hopping diffusion, where particles intermittently escape confinement pockets, providing insights into hydrogel microstructure. Long, highly sampled trajectories enable extraction of kinetic parameters, confinement sizes, and thermodynamic barriers. This study demonstrates 3D-SMARTs ability to probe particle-environment interactions at super-resolution ([~]10 nm in XY and [~]30 nm in Z) in 3D, offering new perspectives on nanoparticle diffusion and the structural dynamics of porous materials, with implications for drug delivery, material science, and biological systems. ToC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/643103v3_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@7c11c4org.highwire.dtl.DTLVardef@1725c22org.highwire.dtl.DTLVardef@fecc4forg.highwire.dtl.DTLVardef@175d33_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗