Biology subjects

Chen, Y.-L.

Publications and source records attributed to Chen, Y.-L..

At least 19 recordsLinked to original sources

bioRxiv2026

AKAP5 and Caveolin-1 organize opposing nanodomains that regulate smooth muscle contraction and blood pressure

TRPV4 ion channels in vascular smooth muscle cells (SMCs) are crucial regulators of blood pressure, and their functional effects are differentially shaped by their signaling partners. However, the mechanisms by which TRPV4 channels are compartmentalized into distinct signaling nanodomains with opposite impacts on blood pressure remain unclear. Here, we identify the scaffolding proteins that compartmentalize TRPV4 channels into discrete nanometer-scale signaling domains at the SMC plasma membrane and define how these nanodomains produce opposing effects on vasoconstriction and blood pressure. We show that AKAP5 anchors a nanodomain linking 1-adrenergic receptors, protein kinase C and TRPV4 channels, thereby driving sympathetic vasoconstriction and blood pressure elevation. In contrast, caveolin-1 promotes a mechanosensitive nanodomain comprising Piezo1, TRPV4, and BK channels that mediates vasodilation and a decrease in blood pressure. In hypertension, AKAP5-dependent constrictor nanodomains are hyperactive, whereas caveolin-1-based dilator nanodomains are hypoactive, shifting the balance toward pathological vasoconstriction. These findings reveal fundamental mechanisms that organize smooth muscle TRPV4 channels into spatially and functionally distinct nanodomains regulating blood pressure and show how disruption of this organization contributes to blood pressure elevation in hypertension.

physiology↗

bioRxiv2026

DHX36 regulates antral follicle development and ovulation as a non-OSF maternal factor by maintaining oocyte homeostasis and supporting OSF delivery

Healthy ovarian follicle development and ovulation require coordinated communication between oocytes and surrounding somatic cells. Although oocyte-secreted factors (OSFs), such as GDF-9 and BMP-15, are established regulators of this communication, the non-OSF maternal factors that support OSF delivery and signaling during late-stage follicle development remain poorly understood. Here, using an oocyte-specific Dhx36 knockout mouse model, we identify the G-quadruplex (G4) helicase DHX36 as a non-OSF maternal factor required for antral follicle development and hormone-induced ovulation. Dhx36 deficiency caused severe defects in granulosa cell proliferation and cumulus expansion, accompanied by impaired activation of SMAD2/3 and SMAD1/5/8, while ERK1/2 activation remained intact. Although the expression of major OSFs was largely unchanged, Dhx36-deficient oocytes exhibited disrupted microvilli and transzonal projections (TZPs), resulting in defective OSF delivery and impaired oocyte-cumulus communication. Proteomic, lipidomic, and ultrastructural analyses further revealed dysregulated phospholipid metabolism, membrane organization, autophagy, and organelle homeostasis, including abnormal lysosomal, mitochondrial, and endoplasmic reticulum structures. Integrative transcriptomic and proteomic analyses identified concordant downregulation of genes involved in these processes, whose promoters were enriched in potential G4 motifs. Consistently, Dhx36 deficiency was associated with reduced RNA polymerase II activity, while pharmacological G4 stabilization impaired transcription of selected genes. Together, these findings establish DHX36 as a maternal regulator that links oocyte intrinsic homeostasis to intercellular communication, suggesting that DHX36-dependent maintenance of membrane and organelle integrity is essential for OSF delivery, cumulus cell function, antral follicle development, and ovulation.

developmental biology↗

bioRxiv2026

Rpd3L Coordinates Chromatin State and Transcription-Replication Conflict Resolution through H3K4 Methylation-Dependent and Independent Mechanisms

Faithful genome duplication requires coordination between transcription and replication. Disruption of this coordination causes transcription-replication conflicts (TRCs), leading to replication stress and genome instability. How chromatin regulators modulate these processes remains unclear. Here, we show that the Rpd3L histone deacetylase complex dynamically modulates chromatin state to control replication fork progression and buffer TRCs in Saccharomyces cerevisiae. Rpd3L is targeted through both histone H3 lysine 4 methylation-dependent recruitment and methylation-independent mechanisms engaged under replication stress. Loss of H3K4 methylation or Rpd3L function promotes histone acetylation, accelerates fork progression through transcribed regions, and increases transcription-associated genome instability. Balanced acetylation at multiple histone lysines is required to stabilize replication forks under stress. While histone deacetylase complexes have been implicated in repairing damaged forks, our findings reveal that Rpd3L acts preemptively to modulate chromatin state and replication dynamics during TRCs, defining a chromatin-based mechanism that safeguards genome stability.

molecular biology↗

bioRxiv2026

Develop a durable, memory-driven, CspZ-targeting Lyme disease vaccine by rationale adjuvant selection

Rational adjuvant selection is a systematic approach based on adjuvant-mediated immunomodulation to identify safe vaccine regimens that enhance protective immunity. Transmitted through ticks and caused by the bacterium Borrelia burgdorferi (Bb), Lyme disease (LD) is the most common vector-borne disease in the Northern hemisphere. There are no effective vaccines, making it suitable for testing the concept of rational adjuvant selection. Here, we formulated our previously developed and effective LD vaccine antigen, CspZ-YAC187S, with different adjuvants suitable for human use; we analyzed the immune response by transcriptomics and tested the vaccine efficacy after Bb infection. We identified Alum-CpG and Alum-Gal to elicit the highest titers of CspZ-YAC187S-dependent protective antibodies and robust levels of protection but through distinct mechanisms of immunomodulation. We demonstrated that immunization with Alum-CpG formulated CspZ-YAC187S provided up to nine months of protective bactericidal antibody titers, as well as recall-memory response to prevent LD after natural infection. Immunity was linked to elevated levels of IgG1 memory cells in the vaccine-triggered immune responses. This work thus identified a durable, memory immunity-driven LD vaccine, ultimately paving the road to understanding the mechanisms of rationale adjuvant selection for vaccine development.

immunology↗

bioRxiv2025

Extending cis-regulatory networks using chromatin-RNA interactions

Cis-regulatory networks are essential for determining gene transcriptional states, yet the mechanisms that mediate cellular signaling and enhancer-promoter communications are not yet well understood. Here, we integrate high-resolution enhancer-promoter interactions obtained using targeted chromosome conformation capture and RNA-DNA contacts from RADICL-seq to uncover the role of RNA in modulating enhancer-promoter interactions. Both datasets were generated from human induced pluripotent cells at different stages across neural differentiation. As expected, most enhancer-promoter interactions were dynamic with only 38% shared across all cell states and 68% of promoter interacting regions overlapped at least one annotated neural enhancer. Integration with RADICL-seq data revealed a 9.3-fold enrichment for cis-interacting DNA regions to associate with at least one RNA. Among 18,346 cis-interacting promoters, only 1,170 (6.3%) lacked any RNA association, whereas 3,702 (28%) showed stable RNA association and 13,579 (74%) displayed dynamic RNA association across differentiation. Promoters associated with RNA engaged with higher number of enhancers and exhibited higher expression levels, while enhancers with RNA associations showed higher levels of chromatin activation marks. Promoters with dynamic RNA association were also more likely to be differentially expressed and enriched for relevant biological processes, phenotypes and diseases. Importantly, RNA-DNA association dynamics correlated strongly with DNA-DNA interaction dynamics; gain of RNA association on enhancers was typically accompanied by enhancer-promoter interaction gain, whereas concurrent RNA association gain on both promoter and enhancers frequently led to interaction loss. The correlation of RNA association on cis-interaction dynamics across differentiation were also captured in the community structure of the DNA-RNA network. Together, our results reveal extensive coupling between RNA-DNA and DNA-DNA networks supporting a coordinating role of RNA in gene regulation.

genomics↗

bioRxiv2025

Oncogenic KRAS regulates secretion of extracellular vesicles and surface membrane charge via regulation of phosphatidylserine in pancreatic cancer

Extracellular vesicles (EVs) have the potential to be used as a liquid biopsy for cancer detection and treatment response assessment. Although the potential of EVs as disease-specific biomarkers has been promising, the rapid and specific enrichment of EVs from body fluids in the clinical setting remains challenging. To address this limitation, we developed a Microfluidic Electrophoresis (MEP) device, that allows label-free enrichment of EVs based on charge from the serum of patients with pancreatic cancer (PaCa). The ability of MEP to enrich anionic EVs was validated using cell line-derived EVs and PaCa serum-derived EVs. We observed a positive correlation between the KRAS status, secretion of EVs, and net negative zeta potential ({zeta}-potential) of EVs. Further analyses identified phosphatidylserine (PS) and extraluminal DNA as molecular determinants of the enhanced anionic nature of PaCa-derived EVs. Overall, this work introduces a new microfluidic device to enrich cancer EVs in circulation with potential for further rapid detection of PaCa.

bioengineering↗

bioRxiv2025

Multi-omics integration uncovers host-microbiota crosstalk underlying sexual differentiation in the shortfin eel Anguilla bicolor pacifica

The global decline in anguillid eel populations has intensified interest in understanding their biology for conservation and aquaculture. While host-gut microbiota interactions are well-characterized in homeotherms, these relationships remain poorly understood in poikilotherms during sexual differentiation. We examined gut microbiota dynamics across developmental stages in the shortfin eel Anguilla bicolor pacifica, which exhibits early sexual differentiation and a relatively short life cycle. Glass eels were cultivated in controlled freshwater conditions for three years, with sampling at key stages: glass eel, elver, sex-undetermined eel, and sex-determined eel. Full-length 16S rRNA gene sequencing revealed significant compositional shifts during development, with higher bacterial richness in adults versus younger eels. Early stages were dominated by Pseudomonadota, while sex-determined adults showed increased Deinococcota abundance. Network analysis identified Deinococcus, Sphingomonas, and Variovorax as key genera in sex-determined eels, with positive correlations between anti-Mullerian hormone gene expression and these taxa. We isolated 66 gut bacterial strains capable of metabolizing sex hormones under microaerobic conditions. These isolates, representing 22 genera across four phyla, demonstrated diverse metabolic capabilities from partial oxidation to complete steroid mineralization. Multiple strains achieved complete estradiol degradation as single isolates--a rare metabolic capability of environmental microorganisms. Comparative genomic analysis revealed widespread steroid-metabolizing genes, with Deinococcus species showing previously unreported hormone degradation capabilities. Our multi-omics analysis demonstrates that gut microbiota composition and function are intimately linked to eel sexual development, suggesting bidirectional host-microbe interactions influencing reproductive physiology. These findings advance understanding of host-microbiota interactions in aquatic vertebrates and provide implications for eel aquaculture and conservation.

microbiology↗

bioRxiv2025

Parameter Efficient Fine-tuning of Transformer-based Masked Autoencoder Enhances Resource Constrained Neuroimage Analysis

Recent innovations in artificial intelligence (AI) have increasingly focused on large-scale foundational models that are more general purpose in contrast to conventional models trained to perform specialized tasks. Transformer-based architectures have become the standard backbone in foundation models across data modalities (image, text, audio, video). There has been a keen interest in applying parameter-efficient fine-tuning (PEFT) methods to adapt these models to specialized downstream tasks in language and vision. These methods are particularly essential for medical image analysis where the limited availability of training data could lead to overfitting. In this work, we evaluated different types of PEFT methods on pre-trained vision transformers relative to typical training approaches, such as full fine-tuning and training from scratch. We used a transformer-based masked autoencoder (MAE) framework, to pretrain a vision encoder on T1- weighted (T1-w) brain MRIs. The pretrained vision transformers were then fine-tuned using different PEFT methods that reduced the trainable model parameters to as few as 0.04% of the original model size. Our study shows that: 1. PEFT methods were competitive with or outperformed the reference full fine-tuning approach and outperformed training from scratch, with only a fraction of the trainable parameters; 2. PEFT methods with a 32% reduction in model size boosted Alzheimers disease (AD) classification by 3% relative to full fine-tuning and 11% relative to a 3D CNN, with only 258 training scans; and 3. PEFT methods performed well on diverse neuroimaging tasks including AD and Parkinsons disease (PD) classification, and "brain-age" prediction based on T1-w MRI datasets - a standard benchmark for deep learning models in neuroimaging; 4. smaller model sizes were competitive with larger models in test performance. Our results show the value of adapting foundation models to neuroimaging tasks efficiently and effectively in contrast to training stand- alone special purpose models.

neuroscience↗

bioRxiv2024

Living xylem cells encode a large number of conserved gene families responsible for vascular sap peptides

Plant long-distance signaling peptides travel through the vascular system to coordinate development and respond to environmental cues, yet their precursor genes and expression origins remain elusive. We characterized 4,804 sap peptide precursor genes in Populus trichocarpa using an integrated approach that combined liquid chromatography tandem mass spectrometry (LC-MS/MS) peptidomics, transcriptomics, and comparative genomics. This study expands the known precursor families from approximately 50 to thousands, the majority of which are conserved across angiosperms. Transcriptome analysis across xylem developmental stages revealed that living xylem cells, typically viewed as precursors to non-living structures, predominantly express these specifically at transitions between primary and secondary growth stages, indicating an active role in plant-wide signaling coordination. The precursor genes show conservation at the transcriptome level and are under strong purifying selection. Our findings provide a comprehensive overview of the gene families encoding sap peptides, redefining xylem as an active participant in plant communication and adaptation.

plant biology↗

bioRxiv2024

Mechanistic insights into structure-based design of a Lyme disease subunit vaccine

The quality of protective immunity plays a critical role in modulating vaccine efficacy, with native antigens often not able to trigger sufficiently strong immune responses for pathogen killing. This warrants creation of structure-based vaccine design, leveraging high-resolution antigen structures for mutagenesis to improve protein stability and efficient immunization strategies. Here, we investigated the mechanisms underlying structure-based vaccine design using CspZ-YA, a vaccine antigen from Borrelia burgdorferi, the bacteria causing Lyme disease (LD), the most common vector-borne disease in the Northern Hemisphere. Compared to wild-type CspZ-YA, we found CspZ-YAI183Y and CspZ-YAC187S required lower immunization frequency to protect mice from LD-associated manifestations and bacterial colonization. We observed indistinguishable human and mouse antigenicity between wild-type and mutant CspZ-YA proteins after native infection or active immunization. This supports our newly generated, high-resolution structures of CspZ-YAI183Y and CspZ-YAC187S, showing no altered surface epitopes after mutagenesis. However, CspZ-YAI183Y and CspZ-YAC187S favored the interactions between helices H and I, consistent with their elevated thermostability. Such findings are further strengthened by increasing ability of protective CspZ-YA monoclonal antibodies in binding to CspZ-YA at a physiological temperature (37{degrees}C). Overall, this study demonstrated enhanced intramolecular interactions improved long-term stability of antigens while maintaining protective epitopes, providing a mechanism for structure-based vaccine design. These findings can ultimately be extended to other vaccine antigens against newly emerging pathogens for the improvement of protective immunity.

immunology↗

bioRxiv2024

Aromatase-independent estrogenesis: Wood-Ljungdahl pathway likely contributed to the emergence of estrogens in the biosphere

Androgen and estrogen, key sex hormones, were long thought to be exclusively produced by vertebrates. The O2-dependent aromatase that converts androgen to estrogen (estrogenesis) has never been identified in any prokaryotes. Here, we report the discovery of anaerobic estrogenesis in a Peptococcaceae bacterium (strain TUW77) isolated from the gut of the great blue-spotted mudskipper (Boleophthalmus pectinirostris). This strain exhibits unprecedented testosterone fermentation pathways, transforming testosterone into estrogens and androstanediol under anaerobic conditions. Physiological experiments revealed that strain TUW77 grows exclusively on testosterone, utilizing the androgenic C-19 methyl group as both the carbon source and electron donor. The genomic analysis identified three copies of a polycistronic gene cluster, abeABC (anaerobic bacterial estrogenesis), encoding components of a classic cobalamin-dependent methyltransferase system. These genes, highly expressed under testosterone-fed conditions, show up to 57% protein identity to the characterized EmtAB from denitrifying Denitratisoma spp., known for methylating estrogen into androgen (the reverse reaction). Tiered transcriptomic and proteomic analyses suggest that the removed C-19 methyl group is completely oxidized to CO2 via the oxidative Wood-Ljungdahl pathway, while the reducing equivalents (NADH) fully reduce remaining testosterone to androstanediol. Consistently, the addition of anthraquinone-2,6-disulfonate, an extracellular electron acceptor, to testosterone-fed TUW77 cultures enabled complete testosterone conversion into estrogen without androstanediol accumulation (anaerobic testosterone oxidation). This discovery of aromatase-independent estrogenesis in anaerobic bacteria suggests that the ancient Wood-Ljungdahl pathway may have contributed to the emergence of estrogens in the early biosphere. SignificanceUsing a testosterone-grown anaerobic bacterium as a model organism, we characterized this unusual anaerobic estrogenesis at the molecular level. Our findings challenge the long-held belief that estrogen production is exclusive to aromatase-containing vertebrates, expanding our understanding of steroid hormone biosynthesis across domains of life. The involvement of ancient strictly anaerobic Peptococcaceae members and the Wood-Ljungdahl pathway suggests that bacterial estrogenesis may predate O2-dependent estrogenesis in vertebrates. Furthermore, the identification of estrogen-producing bacteria in animal guts opens new avenues for potential microbiome-based hypoestrogenism therapies to supplement estrogen in menopausal or ovariectomized females, offering an innovative alternative to current hormone replacement strategies.

microbiology↗

bioRxiv2024

CD4+ tissue resident memory Th17 cells drive IL-17A-mediated joint pathology in Spondyloarthritis

ObjectivesInterleukin (IL)-17A is a key driver of Spondyloarthritis (SpA) joint pathology. We aimed to identify its cellular source in synovial tissue from patients with two forms of SpA namely Axial SpA (AxSpA) and Psoriatic arthritis (PsA). MethodsSynovial tissue from patients with SpA was profiled using single-cell RNA sequencing (scRNA-seq: AxSpA, n=5 and PsA, n=6) or spatial RNA profiling (PsA, n=4). CellPhoneDB was used to infer cell-cell communication. Tissue resident memory Th17 (TRM17)-like cells were generated in vitro using blood memory CD4+ T cells from SpA patients. An epigenetic inhibitor library, siRNA and clustered regularly interspaced short palindromic repeats (CRISPR) were used to identify epigenetic regulator(s) for TRM17. ResultsscRNA-seq showed that CD4+CXCR6+ TRM17 cells are the predominant spontaneous IL17A producers in SpA synovium. Cell-cell communication and single-cell spatial analysis support the interaction between TRM17 and CLEC10A+ dendritic cells, which were activated in SpA. Both sublining and lining fibroblasts in SpA synovium showed evidence of IL-17A activation. In vitro-generated CD4+ TRM17-like cells phenocopied joint tissue TRM17, producing IL-17A/F upon T cell receptor (TCR) stimulation, which was further enhanced by cytokines. Perturbation of BRD1 inhibited the generation of TRM17-like cells. ConclusionsCD4+ TRM17 cells are the predominant source of IL-17A in SpA synovial tissue. TCR stimulation is essential for the secretion of IL-17A by CD4+TRM17-like cells. The epigenetic regulator BRD1 contributes to the generation of CD4+TRM17. Depleting CD4+TRM17 cells in SpA is thus a therapeutic strategy with potential to induce long-term remission. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSInterleukin (IL)-17A plays a key role in the immunopathogenesis of Spondyloarthritis (SpA), but its cellular source in joint tissue has not been determined previously. The induction and accumulation of CD4+ tissue resident memory Th17 (TRM17) cells following the clearance of pathogens has been described in skin, lung and kidney. Whether CD4+ TRM17 cells also accumulate in the joint and contribute to the pathology of SpA is not clear. What this study addsO_LICD4+ TRM17 cells are present in SpA synovial tissue and are the predominant source of IL17A C_LIO_LICD4+ TRM17 cells in SpA joints express IL17A without any in vitro exogenous stimulation C_LIO_LIT cell receptor (TCR) rather than cytokine stimulation is essential for IL-17A production by CD4+ TRM17-like cells C_LIO_LIThe epigenetic regulator BRD1 contributes to the generation of CD4+ TRM17-like cells. C_LI How this study might affect research, practice or policyOur findings identify CD4+ TRM17 cells as the primary source of IL-17A in SpA synovium, a previously unrecognized role for these cells. Key questions remain: How do CD4+ TRM17 cells relate to IL-17A producers in synovial fluid? What mechanisms induce and maintain them in the joint? How do they interact with other cells to promote arthritis? These questions warrant further investigation. In addition, our data suggest that targeting CD4+ TRM17 cells, the "factory" of IL-17A in SpA synovial tissue, has the potential to induce long-term remission, encouraging future efforts to develop new therapies to deplete CD4+ TRM17 cells in SpA.

immunology↗

bioRxiv2024

Evolutionary conserved sap peptides derived from xylem-specific peptide precursors in woody angiosperms

Peptides act as long-distance mobile signals, transported through vascular sap to coordinate complex developmental processes. Since the tissue-specificity of peptide precursor gene expression is critical in determining peptide signaling function, we integrated vascular sap peptidomes with tissue-level transcriptomes to investigate the roles of sap peptides in two economically important woody plants, Populus trichocarpa and Eucalyptus grandis. Xylem exhibited the highest ratio of tissue-specific sap peptide precursor genes. Most of the sap peptides derived from xylem-specific precursor genes of P. trichocarpa and E. grandis were highly conserved throughout woody species selected from different clades in angiosperms, including magnoliids, rosids and asterids in eudicots. To further explore the conservation of these peptides, we examined the sap peptidome of Cinnamomum kanehirae (camphor tree), from the ancient clade with three xylem cell types. Approximately 90% of the peptides from xylem-specific precursors that were conserved between P. trichocarpa and E. grandis, were also conserved in the vascular sap of C. kanehirae, demonstrating a remarkably high conservation of these peptides across woody angiosperms. Most of the sap peptides conserved in these three woody species are also highly conserved across land plants, suggesting that these peptides may contribute to plant terrestrialization. Within the sap peptides from xylem- specific precursor genes, a total of 10 peptides were identical across all three woody plants. This substantial enrichment of xylem-specific precursor-derived peptides, along with their high conservation, suggests that these long-distance mobile peptides play a crucial role in secondary xylem development. One sentence summaryIntegration of sap peptidomic and tissue-level transcriptomic data revealed highly conserved long-distance mobile peptides derived from xylem- specific precursors across woody angiosperms.

evolutionary biology↗

bioRxiv2024

Reversible and effective cell cycle synchronization method for studying stage-specific investigations

The cell cycle is a crucial process for cell proliferation, differentiation, and development. Numerous genes and proteins play pivotal roles at specific cell cycle stages to regulate these events precisely. Studying the stage-specific functions of the cell cycle requires accumulating cell populations at the desired cell cycle stage. Cell synchronization, achieved through the use of cell cycle kinase and protein inhibitors, is often employed for this purpose. However, suboptimal concentrations of these inhibitors can result in reduced efficiency, irreversibility, and undesirable cell cycle defects. In this study, we have optimized effective and reversible techniques to synchronize the cell cycle at each stage in human RPE1 cells, utilizing both fixed high-precision cell cycle identification methods and high-temporal live-cell imaging. These reproducible synchronization methods are invaluable for investigating the regulatory mechanisms specific to each cell cycle stage.

cell biology↗

bioRxiv2024

ImmunoCellCycle-ID: A high-precision immunofluorescence-based method for cell cycle identification

The cell cycle is a fundamental process essential for cell proliferation, differentiation, and development. It consists of four major phases: G1, S, G2, and M. These phases collectively drive the reproductive cycle and are meticulously regulated by various proteins that play critical roles in both the prevention and progression of cancer. Traditional methods for studying these functions, such as flow cytometry, require a substantial number of cells to ensure accuracy. In this study, we have developed a user-friendly, immunofluorescence-based method for identifying cell cycle stages, providing single-cell resolution and precise identification of G1, early S, late S, early G2, late G2, and each sub-stage of the M phase using fluorescence microscopy. This method provides high-precision cell cycle identification and can serve as an alternative to, or in combination with, traditional flow cytometry to dissect detailed substages of the cell cycle in a variety of cell lines.

cell biology↗

bioRxiv2024

A Sap Peptide Conserved across Flowering Plants Positively Regulates Lignin Biosynthesis, Biomass and Immunity

Signaling peptides act as hormones to deliver short- or long-distance intercellular signals to govern complex developmental processes. Identifying endogenous signaling peptides is challenging due to their low abundance and the unknown cleavage sites required for release from precursor proteins, not to mention the investigation of their evolutionary roles across species. Consequently, very few peptides were evolutionarily characterized in vivo, especially long-distance signaling peptides. Here we present current largest peptidomic datasets from six species (maize, camphor tree, tomato, rose gum, soybean and poplar), totaling 12,242 peptides, selected from all representative evolutionary clades of angiosperms, including monocots, magnoliids, rosid eudicots, and asterid eudicots. A sap peptide was found to be identical across all six species and named as ASAP (angiosperm sap peptide), emerging as the most conserved peptide family discovered thus far. ASAP rapidly induces a series of protein phosphorylation involved in a signaling cascade previously reported to regulate lignin biosynthesis, plant growth and plant immunity. Functional assays on ASAP activity demonstrated its capability on the induction of monolignol biosynthesis and lignin deposition. High-throughput phenomic analyses showed that ASAP significantly increased plant above- and below-ground biomass. In addition, ASAP treatment enhanced plant immunity and reduced the number of galls and egg masses against nematode invasion. This study provides insights into the conservation and functional significance of plant long-distance mobile signaling peptides, offering potential applications in crop improvement and disease management strategies.

plant biology↗

bioRxiv2024

Clostridium innocuum, an opportunistic gut pathogen, inactivates host gut progesterone and arrests ovarian follicular development

HighlightsO_LIWe identified Clostridium innocuum as a key player in gut progesterone metabolism. C_LIO_LIProgesterone is converted into epipregnanolone with negligible progestogenic activity. C_LIO_LIWe identified the enzyme and mechanisms of microbial epipregnanolone production. C_LIO_LIC. innocuum caused decreased serum progesterone and follicular arrest in female mice. C_LIO_LIC. innocuum is a causal factor of progesterone resistance in women taking progesterone. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/585140v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@14cceaborg.highwire.dtl.DTLVardef@1946432org.highwire.dtl.DTLVardef@13e46d2org.highwire.dtl.DTLVardef@19b9a25_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG In briefChen et al. identified Clostridium innocuum as a major species involved in gut progesterone metabolism, with epipregnanolone as the main product, and elucidated the molecular mechanisms. C. innocuum inactivates gut progesterone in female mice, leading to decreased circulating progesterone levels. C. innocuum is also a causal factor of follicular arrest. Levels of progesterone, an endogenous female hormone, increase after ovulation; progesterone is crucial in the luteal phase to maintain successful pregnancy and prevent early miscarriage. Both endogenous and exogenous progesterone are recycled between the liver and gut; thus, the gut microbiota regulate host progesterone levels by inhibiting enterohepatic progesterone circulation. Our data indicated Clostridium innocuum as a major species involved in gut progesterone metabolism in women with infertility. C. innocuum converts progesterone into the neurosteroid epipregnanolone (with negligible progestogenic activity). We purified and characterized the corresponding enzyme, namely NADPH-dependent 5{beta}-dihydroprogesterone reductase, which is highly oxygen sensitive and whose corresponding genes are prevalent in C. innocuum. Moreover, C. innocuum-administered female C57BL/6 mice (aged 7 weeks) exhibited decreased serum progesterone levels ([~]35%). Clostridium-specific antibiotics (metronidazole) restored low serum progesterone levels in these mice. Furthermore, prolonged C. innocuum administration (12 weeks) arrested ovarian follicular development in female mice. Cytological and histological analyses indicated that C. innocuum may cause luteal phase insufficiency and affect menstrual regularity. Our findings suggest C. innocuum as a causal factor of progesterone resistance in women taking progesterone.

microbiology↗

bioRxiv2023

Single extracellular vesicle imaging and computational analysis identifiesinherent architectural heterogeneity

Evaluating the heterogeneity of extracellular vesicles (EVs) is crucial for unraveling their complex actions and biodistribution. Here, we identify consistent architectural heterogeneity of EVs using cryogenic transmission electron microscopy (cryo-TEM) which has an inherent ability to image biological samples without harsh labeling methods and while preserving their native conformation. Imaging EVs isolated using different methodologies from distinct sources such as cancer cells, normal cells, and body fluids, we identify a structural atlas of their dominantly consistent shapes. We identify EV architectural attributes by utilizing a segmentation neural network model. In total, 7,576 individual EVs were imaged and quantified by our computational pipeline. Across all 7,576 independent EVs, the average eccentricity was 0.5366, and the average equivalent diameter was 132.43 nm. The architectural heterogeneity was consistent across all sources of EVs, independent of purification techniques, and compromised of single spherical (S. Spherical), rod-like or tubular, and double shapes. This study will serve as a reference foundation for high-resolution EV images and offer insights into their potential biological impact.

bioengineering↗