Biology subjects

Xiao, H.

Publications and source records attributed to Xiao, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Ganoderma lucidum alleviates kidney aging by modulating gut microbiota

BackgroundGanoderma lucidum, a renowned traditional Chinese medicine known for its multiple health benefits, including anti-aging effect, has the ability to influence gut microbiota. However, its specific role in alleviating aging via gut microbiota has not been thoroughly investigated. Here, we explored the impact of G. lucidum sporoderm-broken spore powder (Gl-SBSP) on kidney aging using naturally aged and radiation-induced premature senescence mouse models. MethodsWe analyzed gut microbiota through high-throughput sequencing in naturally aged and radiation-induced premature senescence mice after oral administration of Gl-SBSP. Additionally, untargeted metabolomics of the gut microbiome in naturally aged mice was performed using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analyses. Transcriptomics was employed to systematically measure gene expression levels throughout kidney tissues. ResultsGl-SBSP effectively mitigated aging-related phenotypic changes and significantly alleviated kidney aging, although outcomes were mixed in the irradiation mouse model. Importantly, Gl-SBSP modulated gut bacterial composition, particularly enriching Lachnospiraceae in naturally aged mice and in radiation-induced premature senescence mice with positive prognostic outcomes. Nicotinamide riboside (NR), derived from Lachnospiraceae bacteria, was identified as a potential metabolite that promoted recovery of senescent kidneys and improved renal function, validated through in vitro and in vivo experiments. Transcriptome analysis revealed that NR regulates kidney steroid metabolism in aging. ConclusionOur findings suggest that Gl-SBSPs anti-aging effect is mediated by NR derived from the Lachnospiraceae family, influencing kidney steroid metabolism via the gut-kidney axis. These results provide new insights into the mechanisms underlying the anti-aging properties of Gl-SBSP. AbstractGanoderma lucidum, also known as "Linzhi," is a well-established traditional Chinese medicine renowned for its multiple health benefits and its influence on gut microbiota. In this study, we investigated the anti-aging effect of G. lucidum sporoderm-broken spore powder (Gl-SBSP) through the gut-kidney axis using naturally aged and radiation-induced premature senescence mouse models. Administration of Gl-SBSP not only effectively mitigated aging-related phenotypic changes but also significantly alleviated kidney aging, although outcomes were mixed in the irradiation model. Importantly, Gl-SBSP modulated gut bacterial composition, particularly enriching Lachnospiraceae in naturally aged mice and in radiation-induced premature senescence mice with favorable and long-lasting outcomes. Nicotinamide riboside (NR), derived from Lachnospiraceae bacteria, was identified as a potential metabolite that facilitated the rejuvenation of senescent kidneys and improved renal function through both in vitro and in vivo experiments. Further investigation revealed that NR regulated steroid metabolic process in kidney. Our findings suggest that the anti-aging effect of Gl-SBSP is mediated by NR derived from the Lachnospiraceae bacteria, thereby influencing kidney steroid metabolism through the gut-kidney axis. This study provides novel insights into the anti-aging mechanisms of Ganoderma.

microbiology↗

bioRxiv2024

PPR767 affects plant architecture and drought resistance by modulating complex I activity and ROS content in rice

The RNA-binding proteins (RBPs) encoded by nucleus are essential for the metabolism of RNAs in eukaryotes. The pentatricopeptide repeat (PPR) proteins, a large subset of RBPs, participate in organellar RNA processing for plant development and reproduction. Here, we identified an E-type PPR protein, PPR767, which functions in mitochondria. Knocking out PPR767 resulted in shorter plant height, thinner stems, shorter and narrower blades, and consequently affected yield traits, compared to those of the wild type. PPR767 primarily participated in the editing of 4 sites, nad1-674, nad3-155, nad3-172, and nad7-317. And PPR767 interplayed with MORF1 and MORF8, suggesting the editosome in rice is complicated. Meanwhile, the activity of mitochondrial complex I was decreased, and the structure of mitochondria was compromised in the mutants. Furthermore, mutation of PPR767 influenced rice drought tolerance and the expression levels of genes involved in the reactive oxygen species (ROS) accumulation. These findings suggest that PPR767 guarantees the complex I activity by properly regulating the RNA editing efficiency of mitochondrial genes and affects drought tolerance by modulating ROS content in rice, providing valuable insights into the mechanisms by which PPRs fulfil their functions.

molecular biology↗

bioRxiv2024

Interaction between gene expression and morphokinetic parameters in undisturbed human embryo culture

The clinical in vitro fertilisation (IVF) need for optimal culture conditions and improved selection of human embryos for transfer led to the development of time-lapse systems built into incubators to allow a stable, well-defined and undisturbed culture environment with continual monitoring of embryo development. Clinical data suggest that both undisturbed culture of embryos and selection algorithms based on time-lapse morphometric parameters can potentially improve embryo development and live birth rates. However, there remains a need to validate and understand the mechanisms underlying the potential benefits of the time-lapse technology in IVF. In this study, we compared the gene expression of human embryos grown in an undisturbed time-lapse system with a conventional incubator and showed that there is no fundamental difference in the developmental program of the undisturbed embryos, which provides important reassurance concerning the time-lapse technology. We then performed a network-based integrative analysis based on the undisturbed blastocyst transcriptomes and identified time-lapse parameter correlated genes. These showed cross talk with identified embryo development gene functional modules, suggesting potential molecular mechanisms underlying the clinical predictive capabilities of embryo time-lapse morphokinetic parameters for subsequent live birth. This study suggests methodologies for assessing the impact of additional predictive correlates of value for optimal embryo development and understanding their mechanisms of action.

developmental biology↗

bioRxiv2024

The genomic and epigenomic dynamics of hemizygous genes across crops with contrasting mating systems

Hemizygous genes, which present on only one of the two homologous chromosomes of diploid organisms, have been mainly studied in the context of sex chromosomes and sex-linked genes. However, structural variants (SVs), such as a deletion/insertion of one allele, can lead to hemizygous genes, a phenomenon largely unexplored in plants. Here, we investigated the genomic and epigenomic landscapes of hemizygous genes across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples and four inbred and putatively homozygous genomes. We identified SVs leading to genic hemizygosity. As expected, very few genes (0.01%-1.2%) were hemizygous in the homozygous genomes, representing negative controls. Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes, but consistently elevated for the clonal samples at 13.8% genes, likely reflecting heterozygous SVs accumulation during clonal propagation. Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions and underlying weaker purifying selection. They also had reduced levels of expression, averaging [~]20% of the expression levels of diploid genes, violating the evolutionary model of dosage compensation. We also detected higher DNA methylation levels, in hemizygous genes and transposable elements, which may contribute to the reduced expression of hemizygous genes. Finally, expression profiles showed that hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation and stress responses. Overall, hemizygous genes accumulate in clonally propagated lineages and display distinct genetic, and epigenetic features compared to diploid genes, shedding new insights on genetic studies and breeding programs of clonal crops.

plant biology↗

bioRxiv2024

Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations

INTRODUCTIONMulti-omics studies in Alzheimers disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked African Americans (AA) and Latin Americans (LA), who are disproportionately affected by AD. METHODSTo bridge this gap, Accelerating Medicines Partnership in AD (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTSWe generated multi-omics data and curated and harmonized phenotypic data from AA (n=306), LA (n=326), or AA and LA (n=4) brain donors plus Non-Hispanic White (n=252) and other (n=20) ethnic groups, to establish a foundational dataset enriched for AA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSIONInclusion of traditionally underrepresented groups in multi-omics studies is essential to discover the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD.

neuroscience↗

bioRxiv2024

Exploring Pathogenic Mutation in Allosteric Proteins: the Prediction and Beyond

Allosteric regulation that triggers the functional activity of a protein through conformational changes is an inherent function of the protein in numerous physiological and pathological scenarios. In the post-genomic era, a central challenge for disease genomes is the identification of the biological effects of specific somatic variants on allosteric proteins and the phenotypes they influence during the initiation and progression of diseases. Here, we analyzed more than 38539 mutations observed in 90 human genes with 740 allosteric protein chains. We found that existing allosteric protein mutations are associated with many diseases, but the clinical significance of the majority of mutations in allosteric proteins remains unclear. Next, we developed a machine-learning-based model for pathogenic mutation prediction of allosteric proteins based on the intrinsic characteristics of proteins and the prediction results from existed methods. When tested on the benchmark allosteric protein dataset, the proposed method achieves AUCs of 0.868 and AUPR of 0.894 on allosteric proteins. Furthermore, we explored the performance of existing methods in predicting the pathogenicity of mutations at allosteric sites and identified potential significant pathogenic mutations at allosteric sites using the proposed method. In summary, these findings illuminate the significance of allosteric mutation in disease processes, and contribute a valuable tool for the identification of pathogenic mutations as well as previously unknown disease-causing allosteric-protein-encoded genes.

bioinformatics↗

bioRxiv2024

Pure Nano Genesis: Pioneering Universal Aqueous Nanostrategies from Pure Molecules to Revolutionise Diverse Applications

In this paper, we propose a novel universal approach for the construction of stable and aqueous nanoparticles, Pure Nano systems, comprising solely small conjugated molecules without any excipients. Our experiments confirm that the generation of surface charges plays an essential role during the spontaneous aggregation of conjugated molecules in the process of Pure Nano system fabrication, as it governs growth and confers physiochemical stability to particles at the nano scale. This approach overcomes solubility challenges in highly hydrophobic conjugated molecules by obviating excipients and enabling up to 100% drug loading capacity. Confirmation of this capability stems from the successful preparation of approximately 100 Pure Nano systems, incorporating different combinations of 27 conjugated molecules distinguished by their diverse dissociation types and degrees. The proposed preparation method is robust, simple, fast, and reliable, making it well-suited for large-scale manufacturing due to its array of unique features. This strategy affords a singular, molecular-focused approach, showcasing the intrinsic bioactivity of its constituent molecules while enabling aqueous dispersion for diverse applications. And in vivo experiments confirm the exceptional efficacy of various Pure Nano systems in reinstating dextran sodium sulfate induced acute ulcerative colitis to a healthy state, restoring myocardial ischemia/reperfusion injury to normal levels, and effectively treating cancer in mice with significantly improved median survival rates. This innovative nano drug delivery system represents a groundbreaking advancement with the potential to revolutionise translational nanomedicine. Positioned at the forefront of therapeutic possibilities, it is anticipated to substantially improve the efficacy and safety of nano therapies. This advancement heralds a new era, offering a highly targeted and efficient approach in the treatment of diverse medical conditions.

pharmacology and toxicology↗

bioRxiv2024

N-acetylation of α-synuclein enhances synaptic vesicle clustering mediated by α-synuclein and lysophosphatidylcholine

Post-translational modifications (PTMs) of -synuclein (-syn) such as acetylation and phosphorylation play important yet distinct roles in regulating -syn conformation, membrane binding, and amyloid aggregation. However, how PTMs regulate -syn function in presynaptic terminals remains unclear. Previously, we reported that -syn clusters synaptic vesicles (SV)1, and neutral phospholipid lysophosphatidylcholine (LPC) can mediate this clustering2. Here, based on our previous findings, we further demonstrate that N-terminal acetylation, which occurs under physiological conditions and is irreversible in mammalian cells, significantly enhances the functional activity of -syn in clustering SVs. Mechanistic studies reveal that this enhancement is caused by the N-acetylation-promoted insertion of -syns N-terminus and increased intermolecular interactions on the LPC-containing membrane. Our work demonstrates that N-acetylation fine-tunes -syn-LPC interaction for mediating -syns function in SV clustering.

biophysics↗

bioRxiv2024

The Impact of Anesthesia on Ultrasonic Glymphatic Perturbation Protocol: Alertness, and Glymphatic Influx

We have recently discovered that transcranial low-intensity focused ultrasound can enhance glymphatic transport, which facilitates the removal of waste metabolites from the brain in a preclinical rat model [1]. The central hypothesis was that ultrasound, functioning as a pressure wave, has the potential to influence the convective forces generated by arterial pulsations, which are also pressure waves, serving as the primary mechanism for glymphatic transport. Importantly, our data revealed that (i) the ultrasound protocol (650 kHz at 0.2MPa for 10 minutes to the entire brain) is safe, as histological evaluations showed no parenchymal damage and no difference in levels of neuronal degeneration or astrocytic activation 72 hours after the intervention, and (ii) the required pressure is significantly low, 10 times below FDA-approved limits for diagnostic ultrasound, and can be achieved using existing FDA-approved clinical transcranial focused ultrasound systems, suggesting its ease of translation into clinical applications. However, the study was conducted under specific physiological states with approximately 2.5% isoflurane-induced anesthesia. There is a limitation in fully understanding the potential bioeffects of ultrasound within the glymphatic space across various physiological conditions, primarily because the glymphatic transports efficiency fluctuates with anesthetically induced physiological states. Hence, establishing standardized protocols of ultrasonic glymphatic transport at optimal physiological state is crucial for ensuring consistent, reliable results across research laboratories during the preclinical development of this technique. The primary objective of this study is to evaluate how ultrasonically manipulated glymphatic transport is influenced by different levels of isoflurane-induced anesthetic conditions, including 3% (just above 2.5%), 2% (slightly below 2.5%), and 1.5% (quasi-awake state, resembling the existing clinical practice of ultrasound treatment). Results show that the impact of ultrasound during glymphatic transport depends on the level of anesthesia. It increases alertness in lightly anesthetized animals and improves glymphatic transport, while it induces drowsiness in heavily anesthetized animals, leading to reduced glymphatic transport. The results suggest that lighter anesthesia is beneficial for efficient ultrasonic glymphatic transport, making it more in line with the awake state in current clinical ultrasound treatments, thus advancing the technology closer to clinical translation.

bioengineering↗

bioRxiv2024

Dual-targeted nanoparticulate drug delivery systems for enhancing triple-negative breast cancer treatment

The efficacy of DNA-damaging agents, such as the topoisomerase I inhibitor SN38, is often compromised by the robust DNA repair mechanisms in tumor cells, notably homologous recombination (HR) repair. Addressing this challenge, we introduce a novel nano-strategy utilizing binary tumor-killing mechanisms to enhance the therapeutic impact of DNA damage and mitochondrial dysfunction in cancer treatment. Our approach employs a synergistic drug pair comprising SN38 and the BET inhibitor JQ-1. We synthesized two prodrugs by conjugating linoleic acid (LA) to SN38 and JQ-1 via a cinnamaldehyde thioacetal (CT) bond, facilitating co-delivery. These prodrugs co-assemble into a nanostructure, referred to as SJNP, in an optimal synergistic ratio. SJNP was validated for its efficacy at both the cellular and tissue levels, where it primarily disrupts the transcription factor protein BRD4. This disruption leads to downregulation of BRCA1 and RAD51, impairing the HR process and exacerbating DNA damage. Additionally, SJNP releases cinnamaldehyde (CA) upon CT linkage cleavage, elevating intracellular ROS levels in a self-amplifying manner and inducing ROS-mediated mitochondrial dysfunction. Our results indicate that SJNP effectively targets murine triple-negative breast cancer (TNBC) with minimal adverse toxicity, showcasing its potential as a formidable opponent in the fight against cancer.

cancer biology↗

bioRxiv2024

A comprehensive landscape of the zinc-regulated human proteome

Zinc is an essential micronutrient that regulates a wide range of physiological processes, principally through Zn2+ binding to protein cysteine residues. Despite being critical for modulation of protein function, for the vast majority of the human proteome the cysteine sites subject to regulation by Zn2+ binding remain undefined. Here we develop ZnCPT, a comprehensive and quantitative mapping of the zinc-regulated cysteine proteome. We define 4807 zinc-regulated protein cysteines, uncovering protein families across major domains of biology that are subject to either constitutive or inducible modification by zinc. ZnCPT enables systematic discovery of zinc-regulated structural, enzymatic, and allosteric functional domains. On this basis, we identify 52 cancer genetic dependencies subject to zinc regulation, and nominate malignancies sensitive to zinc-induced cytotoxicity. In doing so, we discover a mechanism of zinc regulation over Glutathione Reductase (GSR) that drives cell death in GSR-dependent lung cancers. We provide ZnCPT as a resource for understanding mechanisms of zinc regulation over protein function.

cell biology↗

bioRxiv2023

Integrative genomics reveals the polygenic basis of seedlessness in grapevine

Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, while the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated four haplotype-resolved telomere-to-telomere (T2T) genomes for two seedless grape cultivars, Thompson Seedless (TS, syn. Sultania) and Black Monukka (BM). Comparative genomics identified a [~]4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genes VvTT16 and VvSUS2 located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, tracing the origin of the seedlessness trait back to Sultania. Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including novel candidate genes, such as three 11S GLOBULIN SEED STORAGE PROTEIN and two CYTOCHROME P450 genes, and well-known genes like VviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 groups related to seed development. Machine learning based genomic selection achieved a remarkable 99% precision in predicting grapevine seedlessness. Our findings highlight the polygenic nature of seedless and provide novel candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.

genetics↗

bioRxiv2023

Uncovering Minimal Pathways in Melanoma Initiation

Cutaneous melanomas are clinically and histologically heterogeneous. Most display activating mutations in Braf or Nras and complete loss of function of one or more tumor suppressor genes. Mouse models that replicate such mutations produce fast-growing, pigmented tumors. However, mice that combine Braf activation with only heterozygous loss of Pten also produce tumors and, as we show here, in an Albino background this occurs even with Braf activation alone. Such tumors arise rarely, grow slowly, and express low levels of pigmentation genes. The timing of their appearance was consistent with a single step stochastic event, but no evidence could be found that it required de novo mutation, suggesting instead the involvement of an epigenetic transition. Single-cell transcriptomic analysis revealed such tumors to be heterogeneous, including a minor cell type we term LNM (Low-pigment, Neural- and extracellular Matrix-signature) that displays gene expression resembling "neural crest"-like cell subsets detected in the fast-growing tumors of more heavily-mutated mice, as well as in human biopsy and xenograft samples. We provide evidence that LNM cells pre-exist in normal skin, are expanded by Braf activation, can transition into malignant cells, and persist with malignant cells through multiple rounds of transplantation. We discuss the possibility that LNM cells not only serve as a pre-malignant state in the production of some melanomas, but also as an important intermediate in the development of drug resistance.

cancer biology↗

bioRxiv2023

In vivo proximity proteomics uncovers palmdelphin (PALMD) as a Z-line-associated mitigator of isoproterenol-induced cardiac injury

Z-lines are core ultrastructural organizers of cardiomyocytes that modulate many facets of cardiac pathogenesis. Yet a comprehensive proteomic atlas of Z-line-associated components remain incomplete. Here, we established an adeno-associated virus (AAV)-delivered, cardiomyocyte-specific, proximity-labeling approach to characterize the Z-line proteome in vivo. We found palmdelphin (PALMD) as a novel Z-line-associated protein in both adult murine cardiomyocytes and human pluripotent stem cell-derived cardiomyocytes. Germline and cardiomyocyte-specific palmd knockout mice were grossly normal at baseline but exhibited compromised cardiac hypertrophy and aggravated cardiac injury upon long-term isoproterenol treatment. By contrast, cardiomyocyte-specific PALMD overexpression was sufficient to mitigate isoproterenol-induced cardiac injury. PALMD ablation perturbed transverse tubules (T-tubules) and their association with sarcoplasmic reticulum, which formed the Z-line-associated junctional membrane complex (JMC) essential for calcium handling and cardiac function. These phenotypes were associated with disrupted localization of T-tubule markers caveolin-3 (CAV3) and junctophilin-2 (JPH2) and the reduction of nexilin (NEXN) protein, a crucial Z-line-associated protein that is essential for both Z-line and JMC structures and functions. PALMD was found to interact with NEXN and enhance its protein stability while the Nexn mRNA level was not affected. Together, this study discovered PALMD as a potential target for myocardial protection and highlighted in vivo proximity proteomics as a powerful approach to nominate novel players regulating cardiac pathogenesis. HighlightsO_LIIn vivo proximity proteomics uncover novel Z-line components that are undetected in in vitro proximity proteomics in cardiomyocytes. C_LIO_LIPALMD is a novel Z-line-associated protein that is dispensable for baseline cardiomyocyte function in vivo. C_LIO_LIPALMD mitigates cardiac dysfunction and myocardial injury after repeated isoproterenol insults. C_LIO_LIPALMD stabilizes NEXN, an essential Z-line-associated regulator of the junctional membrane complex and cardiac systolic function. C_LI

molecular biology↗

bioRxiv2023

Contextualized Networks Reveal Heterogeneous Transcriptomic Regulation in Tumors at Sample-Specific Resolution

Cancers are shaped by somatic mutations, microenvironment, and patient background, each altering gene expression and regulation in complex ways, resulting in heterogeneous cellular states and dynamics. Inferring gene regulatory networks (GRNs) from expression data can help characterize this regulation-driven heterogeneity, but network inference requires many statistical samples, limiting GRNs to cluster-level analyses that ignore intra-cluster heterogeneity. We propose to move beyond coarse analyses of pre-defined subgroups by using contextualized learning, a multi-task learning paradigm that uses multi-view contexts including phenotypic, molecular, and environmental information to infer personalized models. With sample-specific contexts, contextualization enables sample-specific models and even generalizes at test time to predict network models for entirely unseen contexts. We unify three network model classes (Correlation, Markov, Neighborhood Selection) and estimate context-specific GRNs for 7997 tumors across 25 tumor types, using copy number and driver mutation profiles, tumor microenvironment, and patient demographics as model context. Our generative modeling approach allows us to predict GRNs for unseen tumor types based on a pan-cancer model of how somatic mutations affect gene regulation. Finally, contextualized networks enable GRN-based precision oncology by providing a structured view of expression dynamics at sample-specific resolution, explaining known biomarkers in terms of network-mediated effects and leading to novel subtypings that improve survival prognosis. We provide a SKLearn-style Python package https://contextualized.ml for learning and analyzing contextualized models, as well as interactive plotting tools for pan-cancer data exploration at https://github.com/cnellington/CancerContextualized. Significance StatementNetwork estimation is essential for understanding the structure and function of biological systems, but current statistical approaches fail to capture inter-subject heterogeneity or cross-modality information flow, both of which are needed for understanding complex phenotypes and pathologies. We introduce contextualized network inference, leveraging multi-view contextual metadata to capture similarities and differences among heterogeneous observations during network estimation. Sharing information across contexts enables inference at sample-specific resolution, thus quantifying variation between subjects and revealing context-specific network rewiring. Applied to tumor-specific transcriptional network inference using clinical, molecular, and multi-omic data, contextualized networks improve accuracy, generalize to unseen cancer types, and discover novel prognostic tumor subtypes. By tailoring disease models to each sample, contextualized networks promise to enable precision medicine at unprecedented resolution.

bioinformatics↗

bioRxiv2023

Dynamic floral scent profile of Epiphyllum oxypetalum and the cytosolic biosynthesis of trans-Geraniol through mevalonate pathway

O_LIEpiphyllum oxypetalum, a renowned ornamental species in Cactaceae, releases attractive fragrance during its infrequent, transient and nocturnal flowering, the nature and biosynthesis of the volatiles for this floral scent, however, remained unexplored. C_LIO_LIEmploying volatilomic, transcriptomic and biochemical approaches, we systematically characterized the composition, emission dynamics and biosynthesis of E. oxypetalum floral scent. C_LIO_LIFloral scent composition was highly dynamic, with trans-geraniol comprising 72.54% of the total emission at full bloom, followed by benzyl alcohol (12.96%) and methyl salicylate (3.75%), which predominantly emanated from petals and sepals. Transcriptomic analysis and inhibition assay using pathway-specific inhibitors revealed the mevalonate (MVA) pathway as the precursor source for trans-geraniol biosynthesis. Together with elevated expression of both cytosol-localized geraniol pyrophosphate synthase EoGDPS and geraniol synthase EoTPSa1, we elucidated an unusual cytosolic biosynthesis route for geraniol in E. oxypetalum petals. C_LIO_LIOur study on E. oxypetalum scent emission and its biosynthesis offers a comprehensive profile of cactus floral scent profiles and presents a rare case of cytosolic geraniol biosynthesis using MVA pathway-derived substrates. These findings underline the unique metabolism of cactus flower volatiles, which hold a promise to be applied in the development of novel perfumes. C_LI

plant biology↗

bioRxiv2023

Instant Assembly of Collagen for Scaffolding, Tissue Engineering, and Bioprinting

Controllable assembly of cells and tissues offers potential for advancing disease and development modeling and regenerative medicine. The bodys natural scaffolding material is the extracellular matrix, composed largely of collagen I. However, challenges in precisely controlling collagen assembly limit collagens applicability as a primary bioink or glue for biofabrication. Here, we introduce a set of biopatterning methods, termed Tunable Rapid Assembly of Collagenous Elements (TRACE), that enables instant gelation and rapid patterning of collagen I solutions with wide range of concentrations. Our methods are based on accelerating the gelation of collagen solutions to instantaneous speeds via macromolecular crowding, allowing versatile patterning of both cell-free and cell-laden collagen-based bioinks. We demonstrate notable applications, including macroscopic organoid engineering, rapid free-form 3D bioprinting, contractile cardiac ventricle model, and patterning of high-resolution (below 5 (m) collagen filament. Our findings enable more controllable and versatile applications for multi-scale collagen-based biofabrication.

bioengineering↗

bioRxiv2023

Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity

Human SIDT1 and SIDT2 are closely related members of the systemic RNA interference (RNAi)-defective (SID-1) transmembrane family. Both mediate RNA internalization and intracellular transport and are involved in various biological processes. However, the molecular basis of RNA uptake, especially for exogenous small RNAs, remains elusive. Here, we present the cryo-electron microscopy (cryo-EM) structures of human SIDT1 and SIDT2. Both structures reveal the overall architecture of a dimeric arrangement contributed by the {beta}-strand-rich extracellular domain (ECD) and the transmembrane domain (TMD) with 11 passes, highlighting the remarkable structural congruence. The in situ assays confirm that SIDT1 and SIDT2 exist as dimers or higher-order oligomers. We demonstrate that for both SIDT1 and SIDT2, the ECD binds small RNAs, such as dietary plant-derived miRNA, only under acidic conditions. In addition, RNA binding under low pH can trigger higher-order assembly of the ECD dimer, suggesting the potential importance of oligomerization during RNA uptake. Our results illustrate the molecular features of the conserved SID-1 family proteins to elucidate the mechanism of the low pH-dependent activation of RNA uptake mediated by SIDT1 and SIDT2. This study provides a promising understanding of the molecular basis of the nucleic acid delivery platform, which may potentially open new avenues for the design and optimization of RNA-based therapies.

biochemistry↗