Biology subjects

Gao, Y.

Publications and source records attributed to Gao, Y..

At least 307 records · Page 17Linked to original sources

bioRxiv2024

Arl2 Associates with Cdk5rap2 to Regulate Cortical Development via Microtubule Organization

ADP ribosylation factor-like GTPase 2 (Arl2) is crucial for controlling mitochondrial fusion and microtubule assembly in various organisms. Arl2 regulates the asymmetric division of neural stem cells in Drosophila via microtubule growth. However, the function of mammalian Arl2 during cortical development was unknown. Here, we demonstrate that mouse Arl2 plays a new role in corticogenesis via regulating microtubule growth, but not mitochondria functions. Arl2 knockdown leads to impaired proliferation of neural progenitor cells (NPCs) and neuronal migration. Arl2 knockdown in mouse NPCs significantly diminishes centrosomal microtubule growth and delocalization of centrosomal proteins Cdk5rap2 and {gamma}-tubulin. Moreover, Arl2 physically associates with Cdk5rap2 by in silico prediction using AlphaFold Multimer and in vitro binding assays. Remarkably, Cdk5rap2 overexpression significantly rescues the neurogenesis defects caused by Arl2 knockdown. Therefore, Arl2 plays an important role in mouse cortical development through microtubule growth via the centrosomal protein Cdk5rap2.

neuroscience↗

bioRxiv2024

BLADE-ON-PETIOLE interacts with CYCLOIDEA to fine-tune CYCLOIDEA-mediated flower symmetry in Monkeyflowers (Mimulus)

AbstractMorphological novelties, or key innovations, are instrumental to the diversification of the organisms. In plants, one such innovation is the evolution of zygomorphic flowers, which is thought to promote outcrossing and increases flower morphological diversity. We isolated three allelic mutants from two Mimulus species displaying altered floral symmetry and identified the causal gene as the orthologue of Arabidopsis BLADE-ON-PETIOLE. We found that MlBOP and MlCYC2a physically interact and this BOP-CYC interaction module is highly conserved across the angiosperms. Furthermore, MlBOP self-ubiquitinates and suppresses MlCYC2a self- activation. MlCYC2a, in turn, impedes MlBOP ubiquitination. Thus, this molecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression of MlCYC2a, contributing to the formation of bilateral symmetry flowers, a key trait in angiosperm evolution. One Sentence SummaryMolecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression of MlCYC2a, contributing to the bilateral flower symmetry formation.

developmental biology↗

bioRxiv2024

Comparison of urine proteome between obese people and normal weight people

ObjectiveTo explore whether urine proteome can reflect the difference between obese and normal weight people. MethodsUrine samples from obese and normal weight people were collected and identified by non-label quantitative proteomics using high performance liquid chromatography tandem mass spectrometry (LC-MS/MS). The difference proteins of urine proteome between obese and normal weight people were screened for protein function and biological pathway analysis. The urine proteome of obese individuals was compared with that of normal weight people, and the common differential proteins were counted to analyze the protein function and biological pathways. Reported biomarkers of obesity were searched in the urine proteome of obese individuals. Results38 different proteins can be identified in the urine proteome of obese people compared with normal weight people, some of which have been reported to be related to metabolism and obesity, and the biological processes of differential proteins are also related to metabolism and other processes. 8 common differential proteins in the urine proteome of obese individuals and normal weight people, among which some proteins have been reported to be related to metabolism and obesity, and the biological processes of differential proteins are also related to metabolism and other processes. Among the differential proteins in the urine proteome of obese individuals compared with the normal weight people, the reported obesity biomarkers can be matched. ConclusionsThe urine proteome can distinguish the obese people from the normal weight people, and the differential proteins in the urine proteome have key proteins that are known to be related to obesity and metabolism, and the biological processes of differential proteins also related biological processes such as nutrition and metabolism. Urine proteome has the potential to explore the pathogenesis of obesity and provide personalized treatment.

biochemistry↗

bioRxiv2024

Plasticity and evolutionary dynamics of alternative RNA splicing

The ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full-length transcripts enrichment protocol with 5 CAP selection, we sequenced full-length RNA transcripts of 48 individuals from outbred populations and subspecies of Mus musculus, and from the closely related sister species Mus spretus and Mus spicilegus as outgroups. The dataset represents the most extensive full-length high-quality isoform catalog at the population level to date. In total, we reliably identified 117,728 distinct isoforms, of which only 51% were previously annotated. We show that the population-specific distribution pattern of isoforms is phylogenetically informative and reflects the segregating SNP diversity between the populations. We find that ancient housekeeping genes are a major source of the overall isoform diversity, and that the generation of alternative first exons plays a major role in generating new isoforms. Given that our data allow us to distinguish between population-specific isoforms and isoforms that are conserved across multiple populations, it is possible to refine the annotation of the reference mouse genome to a set of about 40,000 isoforms that should be most relevant for comparative functional analysis across species.

genomics↗

bioRxiv2023

Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro

The accurate reconstruction of gene regulation networks (GRNs) from sparse and noisy single-cell or spatial multi-omics data remains a challenge. Here, we present SCRIPro, a comprehensive computational framework that robustly infers GRNs for both single-cell and spatial multi-omics data. SCRIPro first addresses sample sparseness by a density clustering approach. SCRIPro assesses transcriptional regulator (TR) importance through chromatin reconstruction and in silico deletion, referencing 1,292 human and 994 mouse TRs. It combines TR-target importance scores with expression levels for precise GRN reconstruction. Finally, we benchmarked SCRIPro on diverse datasets, it outperforms existing motif-based methods and accurately reconstructs cell type-specific, stage-specific, and region-specific GRNs.

bioinformatics↗

bioRxiv2023

Phosphorylated transcription factor PuHB40 is involved in ROS-dependent anthocyanin biosynthesis in pear exposed to high-light stress

As sessile organisms, plants are increasingly vulnerable to environmental stresses because of global warming and climate change. Stress-induced reactive oxygen species (ROS) accumulation results in plant cell damages and even cell death. Anthocyanins are important antioxidants that scavenge ROS to maintain ROS homeostasis. However, the mechanism underlying ROS-induced anthocyanin accumulation is unclear. In this study, we determined that in pear the HD-Zip I family member PuHB40 mediates ROS-dependent anthocyanin biosynthesis under high-light stress. Specifically, PuHB40 is a transcription factor that induces PuMYB123-like/PubHLH3 complex for anthocyanin biosynthesis. The transcriptional activation by PuHB40 depends on its phosphorylation level, which is regulated by protein phosphatase 2A (PP2A). High ROS contents maintain the phosphorylation of PuHB40 at a high level, while also enhancing PuHB40-induced PuMYB123-like transcription by decreasing the transcription of PuPP2AA2, ultimately leading to increased anthocyanin biosynthesis. Our study revealed the pathway regulating ROS-induced anthocyanin biosynthesis in pear, further clarifying the mechanism underlying abiotic stress-induced anthocyanin biosynthesis, which may have implications for improving plant stress tolerance. IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSVarious abiotic stresses, including high-light intensity, promote the accumulation of anthocyanins in plants, while also activating the production of reactive oxygen species (ROS). Anthocyanins can attenuate the negative effects of high-light stress by acting as antioxidants that restrict ROS accumulation. Several reports have shown that ROS can stimulate anthocyanin accumulation, but whether high-light stress-induced anthocyanin accumulation depends on ROS is undetermined. Additionally, the mechanism underlying ROS-dependent anthocyanin biosynthesis remains unclear. QuestionDoes high-light stress-induced anthocyanin biosynthesis depend on ROS? What is the molecular basis of high-light stress-induced anthocyanin biosynthesis? FindingsHigh-light stress-induced anthocyanin biosynthesis in pear seedlings is dependent on ROS accumulation. PuMYB123-like is the key MYB transcription factor for anthocyanin biosynthesis, while PuHB40 activates anthocyanin biosynthesis in response to ROS under high-light stress. Specifically, PuHB40 activates the transcription of PuMYB123-like, with the encoded protein combining with PubHLH3 to form an MBW complex that promotes anthocyanin biosynthesis. The transcriptional activation by PuHB40 depends on its phosphorylation status, which is regulated by protein phosphatase 2A (PP2A). High ROS levels inhibit the transcription of PuPP2AA2, thereby maintaining the phosphorylation of PuHB40, enhancing the transcriptional activation by PuHB40, inducing PuMYB123-like transcription, and ultimately leading to increased anthocyanin biosynthesis. Next stepsOur future research will focus on whether ROS and the MYB123-like- PuHB40-PP2A regulatory module are also involved in the anthocyanin biosynthesis induced by other abiotic and biotic stresses, which will provide insights into biotic stress-induced anthocyanin biosynthesis and form the theoretical basis for improving fruit coloration.

plant biology↗

bioRxiv2023

Identification of new ciliary signaling pathways in the brain and insights into neurological disorders

Primary cilia are conserved sensory hubs essential for signaling transduction and embryonic development. Ciliary dysfunction causes a variety of developmental syndromes with neurological features and cognitive impairment, whose basis mostly remains unknown. Despite connections to neural function, the primary cilium remains an overlooked organelle in the brain. Most neurons have a primary cilium; however, it is still unclear how this organelle modulates brain architecture and function, given the lack of any systemic dissection of neuronal ciliary signaling. Here, we present the first in vivo glance at the molecular composition of cilia in the mouse brain. We have adapted in vivo BioID (iBioID), targeting the biotin ligase BioID2 to primary cilia in neurons. We identified tissue-specific signaling networks enriched in neuronal cilia, including Eph/Ephrin and GABA receptor signaling pathways. Our iBioID ciliary network presents a wealth of neural ciliary hits that provides new insights into neurological disorders. Our findings are a promising first step in defining the fundamentals of ciliary signaling and their roles in shaping neural circuits and behavior. This work can be extended to pathological conditions of the brain, aiming to identify the molecular pathways disrupted in the brain cilium. Hence, finding novel therapeutic strategies will help uncover and leverage the therapeutic potential of the neuronal cilium.

neuroscience↗

bioRxiv2023

A novel nested gene Aff3ir participates in vascular remodelling by enhancing endothelial cell differentiation in mice

Endothelial integrity in the vasculature is critically maintained by vascular stem/progenitor cells (SPCs) giving rise to endothelial cells (ECs). However, the genes significantly activated during differentiation remain incompletely understood. Based on mouse aorta and vein cDNA library, we unearthed a hitherto unidentified gene nested residing within intron 6 of Aff3, christened as Aff3 intron resident (Aff3ir), upregulated during laminar shear stress-induced ECs differentiation in mouse. Proteomic analysis substantiated the presence of a 45-amino acid(aa) peptide (AFF3IR-ORF1) and 109-aa or 151-aa protein (AFF3IR-ORF2) encoded from two transcript variants. During embryonic development, AFF3IR-ORF1 peaked at E14.5, while AFF3IR-ORF2 displayed a continuous increase until E19.5. In adult mice, AFF3IR-ORF1 was detected in the lung, liver, spleen, and kidney, while AFF3IR-ORF2 was most abundant in the aorta. Furthermore, Western blot and immunofluorescence analyses revealed a specific upregulation of AFF3IR-ORF2, but not AFF3IR-ORF1, three days after femoral artery injury or hindlimb ischemia in vivo. Overexpression of AFF3IR-ORF2 enhanced, while its knockdown attenuated, SPCs differentiation into ECs induced by shear stress or vascular endothelial growth factor in vitro. Notably, the upregulated AFF3IR-ORF2 hindered SPCs proliferation by sequestering minichromosome maintenance complex component 3 in the cytoplasm, thereby shifting the status of SPCs from a pro-proliferation to a pro-differentiation state. In conclusion, our discoveries unveil the novel protein-coding gene Aff3ir as a participant in ECs differentiation, providing fresh insights into the regulation of vascular endothelial integrity.

cell biology↗

bioRxiv2023

A Day in the Life of Arabidopsis: 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms

Functional circadian clock is fundamental to the adaptation and survival of organisms. In land plants, the comprehensive profiling of circadian gene expression at the single-cell level is largely unknown partly due to the challenges in obtaining precisely-timed single cells from plant cells embedded within cell walls. To bridge this gap, we employed single-nucleus RNA sequencing (snRNA-seq) on twelve seedling samples collected at 2-hour intervals over a 24-hour day in Arabidopsis, yielding a total of over 130,000 nuclei. From this data, we found that three cell clusters in the shoot share a coherent rhythm, while more than 3,000 genes display cell-type specific rhythmic expression. Only 19 genes are oscillating in more than ten different cell types, and the majority of them are well-documented core oscillators, suggesting the snRNA-seq circadian data could be used to identify key circadian regulators in a broad range of plant systems. Our data provides the first comprehensive resource for plant circadian rhythms at the single-cell level (hosted at https://zhailab.bio.sustech.edu.cn/sc_circadian).

plant biology↗

bioRxiv2023

Exploring natural genetic variation in photosynthesis-related traits of barley in the field

Optimizing photosynthesis is considered an important strategy for improving crop yields to ensure food security. To evaluate the potential of using photosynthesis-related parameters in crop breeding programs, we measured chlorophyll fluorescence along with growth-related and morphological traits of 23 barley inbreds across different developmental stages in field conditions. The photosynthesis-related parameters were highly variable, changing with light intensity and developmental progression of plants. Yet, the variations in photosystem II (PSII) quantum yield observed among the inbreds in the field largely reflected the variations in CO2 assimilation properties in controlled climate chamber conditions, confirming that the chlorophyll fluorescence-based technique can provide proxy parameters of photosynthesis to explore genetic variations under field conditions. Heritability (H2) of the photosynthesis-related parameters in the field ranged from 0.16 for the quantum yield of non-photochemical quenching to 0.78 for the fraction of open PSII center. Two parameters, the maximum PSII efficiency in light-adapted state ( H2 0.58) and the total non-photochemical quenching ( H2 0.53), showed significant positive and negative correlations, respectively, with yield-related traits (dry weight per plant and net straw weight) in the barley inbreds. These results indicate the possibility of improving crop yield through optimizing photosynthetic light use efficiency by conventional breeding programs.

plant biology↗

bioRxiv2023

Biosurfactant stabilized nanoemulsions as multifunctional magnetically targeted delivery vehicles

Nanoemulsions have been widely used for pharmaceutic applications. However, there remains a significant challenge to functionalize available pharmaceutical surfactants with targeting or reporter moieties to generate next-generation drug delivery systems. Herein, a designed biosurfactant platform technology, based on our library of -helical peptide AM1 derivatives, was used to prepare multifunctional magnetic nanoemulsion drug delivery systems. Key factors such as electrostatic and steric stabilization of the nanoemulsions were determined using this peptide library. Stabilization of the nanoemulsion was achieved by controlled and tunable loading of PEG-functionalized biosurfactant at the oil-water interface. A model drug and iron oxide nanoparticles were incorporated into the oil core to prepare multifunctional nanoemulsions. In vitro cell uptake experiments using an external magnetic field demonstrated controlled rapid uptake of iron oxide loaded nanoemulsions by SKOV3 cancer and RAW 264.7 macrophage cells. SKOV3 cells demonstrated a slower rate of uptake under a magnetic field when compared to RAW 264.7 cells. This work demonstrates a highly adaptable hierarchical nanoemulsion system that can provide a platform to develop effective multifunctional nanomedicines and tools for biomedical insights. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/568750v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@31c3f2org.highwire.dtl.DTLVardef@1376aecorg.highwire.dtl.DTLVardef@14cb0aeorg.highwire.dtl.DTLVardef@1e37a6e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

ADNP Modulates SINE B2-Derived CTCF-Binding Sites during Blastocyst Formation in Mouse

During early embryo development, the nuclear factor CTCF plays a vital role in organizing chromatin structure and regulating transcription. Recent studies have examined the establishment of nucleosome profiles around the CTCF motif sites shortly after fertilization. However, the kinetics of CTCF chromatin occupation in pre-implantation embryos have remained unclear. In this study, we utilized CUT&RUN technology to investigate CTCF occupancy in mouse pre-implantation development. Our findings revealed that CTCF begins binding to the genome prior to zygotic genome activation (ZGA), with a preference for CTCF anchored chromatin loops. Although the majority of CTCF occupancy is consistently maintained, we identified a specific set of binding sites enriched in the mouse-specific short-interspersed element (SINE) family B2, which are restricted to the cleavage stages. Notably, our data suggested that the neuroprotective protein ADNP may counteract the stable association of CTCF at SINE B2-derived CTCF-binding sites.

developmental biology↗

bioRxiv2023

Comparison of urinary proteome in the first two days after mating in male rats

ObjectiveTo explore whether differences between male rats on the next day of mating and on the day of mating can be reflected by the urine proteome. MethodsUrine samples were collected from male Sprague-Dawley rats on the day of mating and the next day of mating. Urine samples were analysed by the free-labelled quantitative proteomics technique of high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS). Differential proteins of the urine proteome were analysed for protein function and biological pathways. Results43 differential proteins were identified by comparing the urine proteome of rats on the next day of mating with that on the day of mating, and nearly two-thirds of the differential proteins were related to spermatogenesis. ConclusionsThe urine proteome has the potential to reflect spermatogenesis without interfering with it.

biochemistry↗

bioRxiv2023

Guanylate cyclase activity of TIR1/AFB auxin receptorsin rapid auxin responses

The plant hormone auxin is perceived by TIR1/AFB receptors, which mediate transcriptional reprogramming via a ubiquitination- and cAMP-dependent mechanism. Same receptors mediate also rapid, non-transcriptional growth responses that are mechanistically less well understood. Here, we demonstrate that TIR1/AFB receptors possess not only adenylate cyclase but also guanylate cyclase activity. Auxin perception independently activates cAMP and cGMP production by TIR1/AFBs in vitro and elevates both cAMP and cGMP levels in planta. Genetic and synthetic biology approaches revealed that AFB1 guanylate cyclase activity is required for the rapid cytosolic Ca2+ transients and root growth inhibition. This unprecedented combination of adenylate and guanylate cyclase activities within a single hormone receptor establishes a new paradigm for how one perception mechanism can mediate distinct downstream responses. One-Sentence SummaryTIR1/AFB auxin receptors possess both, adenylate and guanylate cyclase activities, mediating transcriptional reprogramming and rapid Ca2+-dependent growth responses, respectively.

plant biology↗

bioRxiv2023

Guidelines for performing ribosome profiling in plants including structural analysis of rRNA fragments

Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging methodologies. Furthermore, a common problem when performing Ribo-seq are abundant rRNA fragments that are wastefully incorporated into the libraries and dramatically reduce sequencing depth. To remove these rRNA contaminants, it is common to perform preliminary trials to identify these fragments because they are thought to vary depending on nuclease treatment, tissue source, and plant species. Here, we compile valuable insights gathered over years of generating Ribo-seq datasets from different species and experimental setups. We highlight which technical steps are important for maintaining cross experiment comparability and describe a highly efficient approach for rRNA removal. Furthermore, we provide evidence that many rRNA fragments are structurally preserved over diverse nuclease regimes, as well as across plant species. Using a recently published cryo-electron microscopy (cryo-EM) structure of the tobacco 80S ribosome, we show that the most abundant rRNA fragments are spatially derived from the solvent-exposed surface of the ribosome. The guidelines presented here shall aid newcomers in establishing ribosome profiling in new plant species and provide insights that will help in customizing the methodology for individual research goals.

plant biology↗

bioRxiv2023

The mitochondrial deoxyguanosine kinase is required for female fertility in mice

Mitochondrial homeostasis plays a pivotal role in oocyte maturation and embryonic development. Deoxyguanosine kinase (DGUOK) is a nucleoside kinase that salvages purine nucleoside in the mitochondria and is critical for mitochondrial DNA replication and homeostasis in non-proliferating cells. Dguok loss-of-function mutations and deletions lead to hepatocerebral mitochondrial DNA deletion syndrome. However, its potential role in reproduction remains largely unknown. We found that Dguok knockout results in female infertility. Mechanistically, the deficiency of DGUOK hinders ovarian development and oocyte maturation. Moreover, Dguok deficiency in oocytes caused a significant reduction in mitochondrial DNA and abnormal mitochondrial dynamics, and impaired germinal vesicle breakdown. Only few DGUOK-deficient oocytes were able to extrude the first polar body during in vitro maturation, and these oocytes showed irregular chromosome arrangement and different spindle lengths. In addition, Dguok deficiency elevated reactive oxygen species and accelerated apoptosis in oocytes. Our findings reveal novel physiological roles for the mitochondrial nucleoside salvage pathway in oocyte maturation and implicate that DGUOK is a potential marker for the diagnosis of female infertility.

cell biology↗

bioRxiv2023

Urine proteomic analysis of patients with schizophrenia

We tried to explore the difference of urinary proteome between unmedicated schizophrenia patients and normal people through a small number of cases. The results showed that a total of 35 differential proteins were screened in the schizophrenia group compared with the healthy control group. Through random grouping evaluation, it has 91.4 % credibility. Fifteen of the differentially expressed proteins were reported to be related to schizophrenia mechanism, drug target or nervous system regulation. Among them, the aromatic amino acid decarboxylase related to the pathogenesis of schizophrenia can distinguish all 10 patients and 9 normal people with 100 % accuracy in this study, and the AUC value of 17 proteins is greater than or equal to 0.9. The biological pathways enriched by differentially expressed proteins include ephrin receptor signaling pathway, positive regulation of long-term potentiation (LTP), etc. This study shows that urine proteomics can reflect the difference between schizophrenia and healthy controls, and has the potential as a diagnostic marker.

biochemistry↗

bioRxiv2023

Biosynthesis- and Metabolomics-guided discovery of antimicrobial cyclopeptides against drug-resistant clinical isolates

Antimicrobial resistance remains a significant global threat, contributing significantly to mortality rates worldwide. Ribosomally synthesized and post-translationally modified peptides (RiPPs) have emerged as a promising source of novel peptide antibiotics due to their diverse chemical structures. Here, we reported the discovery of new Avi(Me)Cys-containing cyclopeptide antibiotics through a synergistic approach that combines rule-based genome mining, automated metabolomic analysis, and heterologous expression. We first bioinformatically identified 1,172 RiPP biosynthetic gene clusters (BGCs) responsible for Avi(Me)Cys-containing cyclopeptides from a vast pool of over 50,000 bacterial genomes. Subsequently, we successfully established the connection between three newly identified BGCs and the synthesis of five new peptide antibiotics. Notably, massatide A displayed excellent activity against a spectrum of gram-positive pathogens, including drug-resistant clinical isolates like linezolid-resistant S. aureus and methicillin-resistant S. aureus, with a minimum inhibitory concentration (MIC) of 0.25 g/mL. The remarkable performance of massatide A in an animal infection model, coupled with a low risk of resistance and favorable safety profile, positions it as a promising candidate for antibiotic development. Our study highlights the potential of Avi(Me)Cys-containing cyclopeptides in expanding the arsenal of antibiotics against multi-drug-resistant bacteria, offering promising drug leads in the ongoing battle against infectious diseases.

biochemistry↗