Biology subjects

Le, B.

Publications and source records attributed to Le, B..

16 recordsLinked to original sources

bioRxiv2026

A Novel Biofilm Amyloid Ligand for Caspase-11 Drives Hyperactivation in Dendritic Cells

Bacterial biofilms drive persistent infection and chronic inflammation, yet host sensing of biofilm-derived ligands remains poorly understood. Here we identify curli amyloid, an integral component of Enterobacteriaceae biofilms, as a novel activator of the non-canonical inflammasome in human and mouse dendritic cells (DCs). Curli both primes and activates the inflammasome, directly binding caspase-11 to engage NLRP3 and drive robust IL-1{beta} maturation without pyroptosis, establishing curli as a previously unrecognized trigger of DC hyperactivation. Mechanistically, this non-lytic signaling is marked by limited gasdermin D oligomerization without mitochondrial localization and NINJ1-dependent membrane rupture. Functionally, curli-hyperactivated DCs show enhanced migration to the draining lymph nodes in vivo, suggesting consequent augmented adaptive immunity. Finally, curli-containing biofilms also elicit IL-1{beta} secretion without cell death, identifying bacterial amyloid as a central driver of non-lytic inflammasome activation during immune recognition of biofilms.

immunology↗

bioRxiv2026

A lactate-HIF1-VDR positive feedback loop drives protective SPP1+ macrophage differentiation to inhibit schistosomiasis induced liver fibrosis

Hepatic fibrosis remains a major cause of morbidity and mortality in patients with schistosomiasis without effective therapy. Here we show that vitamin D receptor (VDR) signaling in macrophages is essential for limiting fibrosis, acting through a previously unrecognized metabolic epigenetic circuit. Hepatic macrophages exhibit the highest VDR expression among liver resident cells, and pharmacological VDR activation with paricalcitol selectively expands a protective SPP1+ macrophage subset derived from circulating monocytes. Myeloid specific VDR knockout exacerbates fibrosis and abrogates paricalcitol's hepatoprotective effects, whereas SPP1+ macrophage depletion worsens disease. Mechanistically, VDR activation synergizes with hypoxia and lactate to drive SPP1 expression via glycolytic reprogramming. Moreover, lactate and HIF1alpha cooperatively induce VDR transcription by binding to the Vdr promoter and enhancing histone lactylation, forming a positive feedback loop that amplifies the antifibrotic response. Our findings establish the lactate-HIF1alpha-VDR-SPP1 axis as an endogenous defense mechanism and identify macrophage VDR as a promising therapeutic target for fibrotic liver diseases.

immunology↗

bioRxiv2026

Chemically modified CRISPR enzymes for multi-organ genome editing in vivo

Delivery remains the main obstacle to the development of in vivo genome editing therapies. CRISPR ribonucleoproteins confer high editing activity with transient exposure but lack intrinsic cell entry and targeting. Here we introduce PERCEPT, a delivery platform featuring reversible, covalent modification of CRISPR enzymes. PERCEPT enables modular installation of shielding polymers, amphiphilic delivery peptides and targeting ligands, allowing traceless cytosolic release of the native editor. A formulation incorporating an amphiphilic delivery peptide and the neuron-targeting ligand TET1 edited approximately 56% of striatal volume and 78% of neurons within edited regions after local striatal administration. In the R6/2 Huntington's disease model, PERCEPT mediated targeted editing of the mutant human HTT transgene, reducing mutant huntingtin aggregate burden and shifting local transcriptional programs away from inflammatory and injury-associated states. Tissue-adapted formulations edited 53% of Muller glia following intravitreal delivery, increased skeletal muscle reporter fluorescence tenfold versus unconjugated control following intramuscular injection, and enabled lung airway epithelial cell that persisted for three months following intranasal delivery. Rapid screening revealed that local anatomical and cellular barriers require distinct surface display for optimal editing. These results establish reversible chemical modification as a general strategy for adapting CRISPR enzyme delivery across multiple target tissues in vivo.

bioengineering↗

bioRxiv2026

Beyond copy number: The regulatory architecture of mitochondrial DNA gene expression

Mitochondrial DNA (mtDNA) copy number is widely used as a biomarker for mitochondrial function and disease risk, yet its relationship to mtDNA gene expression - one important functional output - remains poorly understood. Prior studies examining this relationship have largely relied on heterogeneous tissue samples, where confounding by cell-type composition obscures the underlying biology. We rigorously tested this relationship in lymphoblastoid cell lines (LCLs), where we find no correlation between mtDNA copy number and gene expression across 731 individuals, and minimal association across 49 GTEx tissues except whole blood. Using population genetic modeling of heteroplasmy drift between DNA and RNA, we estimate that effectively {approx}50 out of 813 mtDNA templates are transcriptionally active in LCLs, indicating low mtDNA accessibility. This confirms, using an independent method and a different cell type, previous observations in HeLa cells, where mtDNA is largely compacted into nucleoids. Together, our results demonstrate that mtDNA copy number and expression are largely decoupled, and that above a certain rate-limiting threshold, mtDNA accessibility -- rather than absolute copy number -- is the more relevant quantity for explaining inter-individual differences in gene expression. This challenges the interpretation of mtDNA copy number as a proxy for mitochondrial transcriptional output and highlights the need for a more mechanistic understanding of mtDNA copy number associations with disease-relevant traits. Cis- and trans-eQTL mapping further reveals that genetic regulation of mtDNA gene expression operates primarily through post-transcriptional mechanisms rather than transcription initiation, yet despite the high inter-individual variance in mtDNA gene expression, genetic variation underlying mtDNA regulation appears to be under strong selective constraint.

genomics↗

bioRxiv2026

Climate stress priming of juvenile Southern California giant kelp (Macrocystis pyrifera) to thermal extremes

Climate change threatens food production across the globe, creating challenges for food systems. Aquaculture, including seaweed production, is expanding while being threatened by global climate stressors, including increasing extreme events. Marine aquaculture is especially vulnerable to heatwaves, which can rapidly raise temperatures above the physiological limits of some organisms. While several interventions to increase resilience to climate impacts are being explored, priming has emerged as a possible adaptation for seaweeds that maintains genetic diversity but hardens individuals to stressors later in life. California has a developing seaweed sector while also experiencing some of the most extreme marine heatwave conditions on record. We explore temperature impacts and priming - exposing an earlier stage of an organism to a mild stressor to prepare the individual for future stress - on giant kelp Macrocystis pyrifera, an important foundation species along the West Coast of the United States. Our experiments focused on the juvenile sporophyte stage on miniaturized spools, from approximately one week before outplanting size to one week after. First, we determined the reaction norms of M. pyrifera in waters ranging from 5 to 30{degrees}C at the outplanting stage. Next, we explored how priming (heat + or - nutrients) in a hatchery setting prepares M. pyrifera for outplanting to a marine heatwave. To assess experimental outcomes, we took measures of growth, survival, photosynthetic function (Fv/Fm), and carbon and nitrogen assimilation via isotopes. We found temperatures above 20{degrees}C had significant negative impacts on all metrics of performance during the juvenile sporophyte stage. Further, we determined heat priming in conjunction with hatchery level (+) nutrients resulted in overall increased performance when exposed to a marine heatwave. These findings support the continued exploration of priming as a tool for climate resilience and can inform current hatchery practices for aquaculture practitioners looking to improve crop outcomes for this species.

physiology↗

bioRxiv2025

Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening

We profiled developmental-series transcriptome, methylome, and metabolome profiling to reveal extensive epigenetic reprogramming during black raspberry (Rubus occidentalis) fruit ripening. Fruit tissues exhibit globally higher DNA methylation than leaves, particularly in CHG and CHH contexts. Local methylation in all cytosine contexts progressively decreases in promoter regions during ripening, whereas CHG and CHH methylation increase in transposon-rich regions. Two primary methylation transitions--promoter hypomethylation and CHH hypermethylation--govern transcriptional shifts in genes involved in ripening processes. Methyl-binding transcription factors with activation potential likely promote CHH hypermethylation-linked transcriptional activation. Multi-omics integration revealed coordinated anthocyanin accumulation parallels expression of biosynthetic and regulatory genes within coherent networks. Elevated non-CG methylation in heterochromatin coincides with increased transcription of histone variants mediating chromatin compaction, suggesting chromatin remodelers fine-tune accessibility for methyltransferases. Our study highlights both genome-wide and locus-specific epigenetic reprogramming and demonstrates a coordinated interplay between DNA methylation and transcriptional regulation during black raspberry fruit ripening.

genomics↗

bioRxiv2025

Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

The co-evolution of life and Earth has profoundly transformed global biogeochemical cycles over the past 3.5 billion years. These cycles, in turn, have dictated the availability of essential nutrients like phosphorus, nitrogen, and iron, thereby affecting primary productivity and the scale of the Earths biosphere. Despite the critical role of nutrient limitation in shaping the size and scope of the biosphere, significant uncertainties persist about which nutrients were globally limiting at various points in Earth history. Here, we use a phylogenomic approach to trace the origin and spread of genes associated with nutrient limitation over time. We show that genes associated with phosphorus limitation emerged relatively early in lifes history, whereas genes associated with nitrogen limitation emerged later, closer to the Great Oxidation Event. In terms of iron limitation, we present novel evidence that siderophores, compounds that facilitate iron uptake, may have arisen as early as the Archean. Overall, our results have important implications for understanding how the geosphere has influenced the scale and extent of life on Earth for the past 4 billion years.

bioinformatics↗

bioRxiv2024

Rat primary cortical cell tri-culture to study effects of amyloid-beta on microglia function

IntroductionThe etiology and progression of sporadic Alzheimers Disease (AD) have been studied for decades. One proposed mechanism is that amyloid-beta (A{beta}) proteins induce neuroinflammation, synapse loss, and neuronal cell death. Microglia play an especially important role in A{beta} clearance, and alterations in microglial function due to aging or disease may result in A{beta} accumulation and deleterious effects on neuronal function. However, studying these complex factors in vivo, where numerous confounding processes exist, is challenging, and until recently, in vitro models have not allowed sustained culture of microglia, astrocytes and neurons in the same culture. Here, we employ a tri-culture model of rat primary neurons, astrocytes, and microglia and compare it to co-culture (neurons and astrocytes) and mono-culture enriched for microglia to study microglial function (i.e., motility and A{beta} clearance) and proteomic response to exogenous A{beta}. MethodsWe established cortical co-culture (neurons and astrocytes), tri-culture (neurons, astrocytes, and microglia), and mono-culture (microglia) from perinatal rat pups. On days in vitro (DIV) 7 - 14, the cultures were exposed to fluorescently-labeled A{beta} (FITC-A{beta}) particles for varying durations. Images were analyzed to determine the number of FITC-A{beta} particles after specific lengths of exposure. A group of cells were stained for {beta}III-tubulin, GFAP, and Iba1 for morphological analysis via quantitative fluorescence microscopy. Cytokine profiles from conditioned media were obtained. Live-cell imaging with images acquired every 5 minutes for 4 hours was employed to extract microglia motility parameters (e.g., Euclidean distance, migration speed, directionality ratio). Results and discussionFITC-A{beta} particles were more effectively cleared in the tri-culture compared to the co-culture. This was attributed to microglia engulfing FITC-A{beta} particles, as confirmed via epifluorescence and confocal microscopy. Adding FITC-A{beta} significantly increased the size of microglia, but had no significant effect on neuronal surface coverage or astrocyte size. Analysis of the cytokine profile upon FITC-A{beta} addition revealed a significant increase in proinflammatory cytokines (TNF-, IL-1, IL-1{beta}, IL-6) in tri-culture, but not co-culture. In addition, A{beta} addition altered microglia motility marked by swarming-like motion with decreased Euclidean distance yet unaltered speed. These results highlight the importance of cell-cell communication in microglia function (e.g., motility and A{beta} clearance) and the utility of the tri-culture model to further investigate microglia dysfunction in AD.

neuroscience↗

bioRxiv2024

A developmental brain-wide screen identifies retrosplenial cortex as a key player in the emergence of persistent memory

Memories formed early in life are short-lived while those formed later persist. Recent work revealed that infant memories are stored in a latent state. But why they fail to be retrieved is poorly understood. Here we investigated brain-wide circuit mechanisms underlying infantile amnesia. We performed a screen that combined contextual fear conditioning, activity-dependent neuronal tagging at different postnatal ages, tissue clearing and light sheet microscopy. We observed striking developmental changes in regional activity patterns between infant, juvenile, and adult mice, including changes in the retrosplenial cortex (RSP) that aligned with the emergence of persistent memory. We then performed a series of targeted investigations of RSP structure and function across development. Chronic chemogenetic reactivation of tagged RSP ensembles during the week after learning enhanced memory in adults and juveniles, but not in infants. However, after 33 days, reactivating infant-tagged RSP ensembles recovered forgotten memories. Changes in the developmental functions of RSP memory ensembles were accompanied by changes in dendritic spine density and the likelihood that those ensembles could be reactivated by contextual cues. These studies show that RSP ensembles store latent infant memories, reveal the time course of RSP functional maturation, and suggest that immature RSP functional networks contribute to infantile amnesia.

neuroscience↗

bioRxiv2023

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk post-mortem adult brain tissue. However, many brain-trait associated loci have unknown cellular or molecular function. These genetic variants may exert context-specific function on different molecular phenotypes including post-transcriptional changes. Here, we identified genetic regulation of RNA-editing and alternative polyadenylation (APA), within a cell-type-specific population of human neural progenitors and neurons. More RNA-editing and isoforms utilizing longer polyadenylation sequences were observed in neurons, likely due to higher expression of genes encoding the proteins mediating these post-transcriptional events. We also detected hundreds of cell-type-specific editing quantitative trait loci (edQTLs) and alternative polyadenylation QTLs (apaQTLs). We found colocalizations of a neuron edQTL in CCDC88A with educational attainment and a progenitor apaQTL in EP300 with schizophrenia, suggesting genetically mediated post-transcriptional regulation during brain development lead to differences in brain function.

genomics↗

bioRxiv2023

Caspase-2 is essential for proliferation and self-renewal of nucleophosmin-mutated acute myeloid leukemia.

Mutation in nucleophosmin (NPM1) causes relocalization of this normally nucleolar protein to the cytoplasm (NPM1c+). Despite NPM1 mutation being the most common driver mutation in cytogenetically normal adult acute myeloid leukemia (AML), the mechanisms of NPM1c+-induced leukemogenesis remain unclear. Caspase-2 is a pro-apoptotic protein activated by NPM1 in the nucleolus. Here, we show that caspase-2 is also activated by NPM1c+ in the cytoplasm, and DNA damage-induced apoptosis is caspase-2-dependent in NPM1c+ AML but not in NPM1wt cells. Strikingly, in NPM1c+ cells, loss of caspase-2 results in profound cell cycle arrest, differentiation, and down-regulation of stem cell pathways that regulate pluripotency including impairment in the AKT/mTORC1 and Wnt signaling pathways. In contrast, there were minimal differences in proliferation, differentiation, or the transcriptional profile of NPM1wt cells with and without caspase-2. Together, these results show that caspase-2 is essential for proliferation and self-renewal of AML cells that have mutated NPM1. This study demonstrates that caspase-2 is a major effector of NPM1c+ function and may even be a druggable target to treat NPM1c+ AML and prevent relapse.

cancer biology↗

bioRxiv2022

Life history strategies and niches of soil bacteria emerge from interacting thermodynamic, biophysical, and metabolic traits

Efficient biochemical transformation of belowground carbon by microorganisms plays a critical role in determining the long-term fate of soil carbon. As plants assimilate carbon from the atmosphere, up to 50% is exuded into the area surrounding growing roots, where it may be transformed into microbial biomass and subsequently stabilized through mineral associations. However, due to a hierarchy of interacting microbial traits, it remains elusive how emergent life-history strategies of microorganisms influence the processing of root exudate carbon. Here, by combining theory-based predictions of substrate uptake kinetics for soil bacteria and a new genome-informed trait-based dynamic energy budget model, we predicted life history traits and trade-offs of a broad range of soil bacteria growing on 82 root exudate metabolites. The model captured resource-dependent trade-offs between growth rate (power) and growth efficiency (yield) that are fundamental to microbial fitness in communities. During early phases of plant development, growth rates of bacteria were largely constrained by maximum growth potential, highlighting the predictive power of genomic traits during nutrient-replete soil conditions. In contrast, selection for efficiency was important later in the plant growing season, where the model successfully predicted microbial substrate preferences for aromatic organic acids and plant hormones. The predicted carbon-use efficiencies for growth on organics acids were much higher than typical values observed in soil. These predictions provide mechanistic underpinning for the apparent efficiency of the microbial route to mineral stabilization in the rhizosphere and add an additional layer of complexity to rhizosphere microbial community assembly.

ecology↗

bioRxiv2022

Arabidopsis AAR2, a conserved splicing factor in eukaryotes, acts in microRNA biogenesis

MicroRNAs (miRNAs) play an essential role in plant growth and development, and as such, their biogenesis is fine-tuned via regulation of the core microprocessor components. Here, we report that Arabidopsis AAR2, a homolog of a U5 snRNP assembly factor in yeast and humans, not only acts in splicing but also promotes miRNA biogenesis. AAR2 interacts with the microprocessor component HYPONASTIC LEAVES1 (HYL1) in the cytoplasm, nucleus and dicing bodies. In aar2 mutants, abundance of nonphosphorylated HYL1, the active form of HYL1, and the number of HYL1-labeled dicing bodies are reduced. Primary miRNA (pri-miRNA) accumulation is compromised despite normal promoter activities of MIR genes in aar2 mutants. RNA decay assays show that the aar2-1 mutation leads to faster degradation of pri-miRNAs in a HYL1-dependent manner, which reveals a previously unknown and negative role of HYL1 in miRNA biogenesis. Taken together, our findings reveal a dual role of AAR2 in miRNA biogenesis and pre-mRNA splicing. SignificanceIn yeast and humans, AAR2 is involved in pre-mRNA splicing through regulating U5 snRNP assembly. This study shows that Arabidopsis AAR2 promotes microRNA (miRNA) accumulation in addition to its conserved role in pre-mRNA splicing. AAR2 is associated with the microprocessor component HYL1 and promotes its dephosphorylation to produce the active form in miRNA biogenesis. The study also reveals a previously unknown role of HYL1 in causing the degradation of the primary precursors to miRNAs (pri-miRNAs) and a role of AAR2 in protecting pri-miRNAs from HYL1-depedent degradation. Taken together, our findings provide new insights into the role of a conserved splicing factor in miRNA biogenesis in plants.

plant biology↗

bioRxiv2020

Title: Two-Photon Microperimetry: A media opacity-independent retinal function assay

Humans perceive light in the visible portion of electromagnetic radiation. However, visible light is scattered and attenuated by optical media opacities. Because all conventional visual function tests rely on visible light, test results are reduced in patients with optical media opacities like corneal scars, cataracts, and vitreous hemorrhages. Infrared (IR) light has greater penetrance through tissue than visible light. Two-photon IR visual stimulation, a recently pioneered technology, should enable testing of retinal visual function and produce results that are less susceptible to media opacities. The effects of simulated media opacities on visual performance in young healthy volunteers and the change in visual function in healthy phakic patients of two age ranges (20-40 and 60-80-year-old) were studied using conventional testing and 2-photon infrared visual stimulation. All subjects completed visual function testing using cone contrast threshold (CCT) testing, conventional microperimetry, visible light microperimetry from a novel device (2PM-Vis), and infrared 2-photon microperimetry (2PM-IR). Retinal sensitivity measured by 2PM-IR demonstrated lower variability than all other devices relying on visible spectrum stimuli. Retinal sensitivity decreased proportionally with the transmittance of light through each filter. CCT scores and retinal sensitivity decreased with age in all testing modalities. Visible spectrum testing modalities demonstrated larger test result differences between young and old patient cohorts; this difference was inversely proportional to the wavelength of the visual function test. 2PM-IR mitigates media opacities which may mask small differences in retinal sensitivity when tested with conventional visual function testing devices.Competing Interest StatementGrazyna Palczewska has a conflict of interest in this study, as she is an employee of Polgenix, Inc.View Full Text

bioengineering↗

bioRxiv2020

Quantifying Color Vision Changes Associated with Cataracts Using Cone Contrast Thresholds

PurposeThe cone contrast threshold (CCT) test quantified color vision changes in subjects of all ages and those undergoing cataract surgery. MethodsTwenty-four healthy volunteers from two cohort studies performed CCT using best corrected visual acuity, filters, mydriasis, and pinhole correction. Retrospective cross-sectional study of patients seen in eye clinics evaluated the relationship between age and color vision, and age and lens status in 355 eyes. Lastly, 25 subjects performed CCT before and after cataract surgery. ResultsCCT scores were most reliable in the non-mydriatic condition without pinhole correction. Progressively dense brown filters produced small but significant reductions in S-cone sensitivity. Linear regression analysis of phakic subjects showed a decline for all cone classes with age. Rate of decline was greater for S-cones (slope (95% CI) = -1.09 (-1.23, 0.94)) than M-cones (slope (95% CI) = -0.80 (-0.95, -0.66)) and L-cones (slope (95% CI) = -0.66 (-0.81, - 0.52)). CCT scores increased for S-cones but reduced for L- and M-cones in pseudophakic subjects compared to phakic patients. CCT scores after cataract surgery increased for S-cones, M-cones, and L-cones by 33.0 (p<0.001), 24.9 (p=0.001), and 22.0 (p=0.008). ConclusionsCCT assessment allows for clinically practical quantitation of color and contrast vision improvement after cataract surgery and aging patients who note poor vision despite good visual acuity. Translational RelevanceCCT testing, historically used in research, is now a clinically practical tool to evaluate age and cataract related changes in color and contrast vision and routinely quantify vision beyond black and white visual acuity testing.

pathology↗

bioRxiv2019

A draft genome sequence of the miniature parasitoid wasp, Megaphragma amalphitanum

Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals to conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect - the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, the gene content of M. amalphitanum compared to other chalcid wasps is remarkably conserved. Among the very rare cases of apparent gene loss is centrosomin, which encodes an important centrosome component; the absence of this protein might be related to the large number of anucleate neurons in M. amalphitanum. Intriguingly, we also observed significant changes in M. amalphitanum transposable element dynamics over time, whereby an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Thus, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.

genomics↗