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Biology subjects

Zhao, Z.

Publications and source records attributed to Zhao, Z..

At least 145 records · Page 8Linked to original sources

Mycobiome analysis of electronic cigarettes reveals a reservoir of pathogenic yeasts

Research on the health impacts of e-cigarettes has focused on non-infectious manifestations. Given their enclosed plastic design and temperature fluctuations, we hypothesized that e-cigarettes are colonized by pathogenic microbes, thereby contributing to lung disease in users. Using sequencing and culture techniques of the devices and mouthwash of 25 users, we found only a small subset of mouthpieces to contain bacteria, whereas most were abundantly colonized with fungi that were distinct from the oral mycobiota, including the genera Rhodotorula, Aureobasidium, Cystobasidium, and Meyerozyma. Chronic exposure to the most frequently isolated pathogen, Cystobasidium minutum, resulted in mucus hypersecretion and obstructive lung disease in mice, characteristics of chronic bronchitis. We conclude that e-cigarettes are frequently colonized with fungal organisms capable of causing lung disease.

molecular biology↗

CCB79 is a primate-specific cilium initiation factor essential to maintain neural progenitor diversity in developing brain tissue.

Identifying the genes that regulate the accurate spatiotemporal diversity of neural progenitor cells (NPCs) helps to understand the mechanisms of human neocortex expansion. In primate brains, an additional intermediate progenitor layer, the outer subventricular zone (oSVZ), facilitates the expansion of the neocortex. Here, we identify an uncharacterized gene, KIAA0408, and show that its expression is enriched in intermediate progenitors. Removing KIAA0408 in human-induced pluripotent stem cell (iPSC)-derived brain organoids results in an impaired cortical organization characterized by abnormal cell fate and patterning defects, including the depletion of intermediate and ventral progenitors. Molecularly, KIAA0408 codes for a 79-kilodalton centriolar distal appendage protein (DAP) that controls cilium biogenesis (hereafter CCB79). CCB79 forms a complex with other DAP components and specifically localizes in the DAP at the onset of ciliogenesis, and its absence blocks ciliogenesis. Mechanistically, progenitors in 3D brain tissues are unable to form cilia, which induces aberrant hedgehog signaling and causes premature differentiation. Finally, human CCB79, rather than the mouse ortholog, rescues cilia defects, suggesting that CCB79 has undergone rapid evolution from rodents to primates to fine-tune ciliogenesis for proper brain development.

neuroscience↗

Developmental and Environmental Stability of Candidate Reference Genes in the Wild Bee Ceratina calcarata

Quantitative real-time PCR (RT-qPCR) is a widely used method for measuring gene expression, but its accuracy depends on the use of stable reference genes for data normalization. In this study, we evaluated the expression stability of seven candidate reference genes (RPS18, RPS5, RPL32, RPL8, EF-1, {beta}-Actin, and GAPDH) in the small carpenter bee Ceratina calcarata across developmental stages (larvae, pupae, adults) and different landscape environments (conventional farms, organic farms, and roadside sites). Using four analytical algorithms, GeNorm, NormFinder, BestKeeper, and the comparative {Delta}Ct method, we identified RPS18 and RPL8 as the most stable reference genes under varying biological and environmental conditions. These findings were further supported by RefFinder, which integrates results from all algorithms. Our study provides the first validated reference genes for C. calcarata, enabling more accurate and reproducible gene expression analysis in this ecologically important wild bee species. This work will support future research in pollinator biology, environmental stress responses, and conservation genomics.

genomics↗

A high-quality bread wheat genome unravels adaptive evolution of wheat end-use quality

Understanding the genetics of superior dough performance is essential for improving wheat end-use quality. Here, we presented a de novo assembly of the genome of JM44, a Chinese wheat cultivar known for its exceptional end-use quality. The JM44 genome achieved reference-level quality (QV = 66.74), depicting a complete picture of complex regions containing gluten genes. Our microsynteny analysis across the Triticum-Aegilops complex showed that high-molecular-weight glutenin subunits (HMW-GSs) loci are highly conserved, while low-molecular-weight glutenin subunits (LMW-GSs) and -/{beta}-gliadins exhibited greater structural variation. These variable loci appear to have been preferentially selected by humans and contributed substantially to the evolution of wheat quality traits. Moreover, we observed that epistatic interactions between gluten genes are strong in modern cultivars, but markedly weaker in landraces, indicating the importance of epistatic selection during modern breeding. Our findings shed light on the genomics and evolution of wheat quality traits, providing valuable guidance for future breeding efforts.

genomics↗

The distribution of the time to the most recent pairwise genetic common ancestor of a set of sampled genomes

In a sample of chromosomes from a recombining population, each pair of individuals will have different most recent common genetic ancestors at different loci. We consider the distribution of the time to the most recent of these most recent common ancestors--the most recent time at which any pair of individuals in the sample share a common genetic ancestor at any locus. We use simple heuristic arguments, formal calculations, and coalescent simulations to find that as long as the chromosomal map length R is sufficiently long and the sample size n is not too large, the distribution of this time is peaked around a characteristic value. This value has the unusual scaling [Formula], where N is the effective size of the population.

evolutionary biology↗

Cryo-EM structures of naturally occurring dimeric photosystem II complexes lacking the Mn4CaO5 cluster

Robust oxygenic photosynthesis requires the efficient assembly and repair of the multi-subunit oxygen-evolving photosystem II (PSII) complex. Previous electron cryo-microscopy (cryo-EM) structures of PSII assembly/disassembly intermediates have relied on the analysis of deletion mutants or removal of PSII subunits in vitro. Here we have determined the cryo-EM structures of naturally occurring dimeric PSII intermediates from the cyanobacterium Thermosynechococcus vestitus at a resolution of 2.2 [A]. These intermediates contain inactive dimers lacking the oxygen-evolving complex (OEC) and semi-active dimers with the OEC present in one of the two monomers. Our structural data provide a mechanism for how assembly and disassembly of the Mn4CaO5 cluster is coordinated with the binding and release of the extrinsic proteins: restructuring of the C-terminal tail of D1 subunit during assembly or disassembly of the Mn cluster triggers conformational changes in D2, CP47 and CP43 to drive the binding/release of the extrinsic proteins. A combination of structural and mass spectrometry data indicates that the inactive PSII complexes are disassembly complexes and that oxidation of D1-His332, a monodentate ligand to one of the Mn ions of the OEC, is an early event in the photoinactivation of PSII.

biochemistry↗

A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation

Long-range RNA-RNA pairing impacts the genome structure and function of SARS-CoV-2 variants. To understand the structure and function relationships of different SARS-CoV-2 variants that have emerged during the COVID-19 pandemic, we performed high-throughput structure probing and modelling of the genomic structures of the wildtype (WT), Alpha, Beta, Delta and Omicron variants of SARS-CoV-2. We observed that genomes of SARS-CoV-2 variants are generally structurally conserved, and that single-nucleotide variations and interactions with RNA binding proteins can impact RNA structures across the viruses. Importantly, using proximity ligation sequencing, we identified many conserved ultra-long-range RNA-RNA interactions, including one that spans more than 17 kb in both the WT virus and the Omicron variant. We showed that mutations that disrupt this 17 kb long-range interaction reduce viral fitness at later stages of its infection cycle, while compensatory mutations partially restore virus fitness. Additionally, we showed that this ultra-long-range RNA-RNA interaction structure binds directly to ADAR1 to alter the RNA editing levels on the viral genome. These studies deepen our understanding of RNA structures in the SARS-CoV-2 genome and their ability to interact with host factors to facilitate virus infectivity.

genomics↗

An active Unc13A is Reboundless in sleep homeostasis

One of the major characteristics of sleep is homeostatic sleep rebound following sleep loss. While the molecular mechanisms of baseline sleep regulation have been intensively studied, a specific molecular understanding of sleep rebound remains elusive. Here, we show that a constitutively active form of the Munc13-family presynaptic release factor Unc13A, which lacks the inhibitory Ca2+/calmodulin interaction domain (Unc13AWRWR), dominantly suppressed sleep rebound upon acute sleep deprivation, leading to a nearly complete elimination of recovery sleep ("reboundless"). In contrast, baseline sleep remained largely normal. Through a genetic modifier screen, we found that this dominant "reboundless" phenotype of Unc13AWRWR was rescued by a partial loss of Snap, a cofactor of NSF required for disassembly and recycling of post-fusion cis-SNARE complex. Given that Unc13A promotes fusion-competent trans-SNARE complex formation, these findings suggest that sleep rebound may depend on a delicate balance between SNARE complex assembly and recycling. Additionally, we found that expression of a human disease-associated active Unc13A (Unc13APL) variant attenuated baseline and rebound sleep. Since both Unc13AWRWR and Unc13APL were shown to promote presynaptic release probability (Pr), we speculate that Unc13A suppresses recovery sleep likely by increasing Pr and subsequently enhancing synaptic transmission, probably through elevated trans-SNARE formation and efficient cis-SNARE recycling. Taken together, our data demonstrate a fundamental role of Unc13A and SNARE dynamics in sleep homeostasis.

neuroscience↗

Genome Mining and Characterization of a Heme-Dependent Enzyme Catalyzing Intermolecular Nitrogen-Nitrogen Bond Formation in Hydrazinosuccinic Acid Biosynthesis

Nitrogen-nitrogen (N-N) bond-forming enzymes are rare but play vital roles in both primary and secondary metabolism. Guided by a nitric oxide synthase (NOS)-based genome mining strategy, we report the discovery and characterization of a new heme-dependent enzyme system that catalyzes intermolecular N-N bond formation. Using both in vivo and in vitro reconstitution approaches, we demonstrated that a protein complex, comprising a heme enzyme and a 2[4Fe-4S] ferredoxin partner, mediates the coupling of the -amine group of L-aspartate with inorganic nitrogen oxide species, such as nitrite or nitric oxide, to generate hydrazinosuccinic acid, a key biosynthetic precursor in several natural product pathways. Structural modeling and site-directed mutagenesis suggest a plausible catalytic mechanism involving the formation of a reactive nitrogen intermediate, potentially a heme-bound nitrene species. These findings reveal a new family of N-N bond-forming biocatalysts that leverage inorganic nitrogen sources, offering valuable tools for genome mining and the synthetic biology.

biochemistry↗

The bifunctional dynamin-like GTPase switch DynAB modulates both vegetative and sporulation cell division in Streptomyces.

As part of their complex developmental lifecycle, the multicellular filamentous bacteria Streptomyces have evolved two modes of cell division distinct from binary fission. In vegetative cell division, irregularly spaced cross-walls form within vegetative hyphae, whereas in sporogenic hyphae, regularly spaced sporulation septa form synchronously, leading to spore formation. However, the mechanisms controlling these processes largely remain unknown. The bacterial dynamin-like protein pair DynAB was previously reported to be a component of sporulation septa. Here, we reveal that DynA and DynB have critical roles in both cell division modes, regulating the formation of sporulation septa and cross-walls, with the Streptomyces cell division protein SsgB modulating their activities. dynAB deletion and overexpression, respectively, increased and abrogated cross-wall formation in vegetative hyphae, and Streptomyces DynAB also inhibited cell division in Escherichia coli, resulting in formation of unicellular filamentous cells and suggesting an ancient and conserved function for these proteins. Notably, SsgB could relieve the inhibition of cell division by DynAB in both Streptomyces and E. coli. In contrast to DynAB, SsgB overexpression generated spore-like compartments in vegetative hyphae, a phenomenon that required disruption of the DynAB complex. Fluorescent tags revealed dynamic localization of DynAB during development, and further analyses indicated that, in sporogenic hyphae, the timing of DynAB expression, their GTP-binding activity, and interaction with SsgB were associated with the synchronous initiation of sporulation septation. Our findings establish DynAB as an integrator of spatiotemporal cues in bacterial multicellularity and provide insights into the evolution of complex cell cycle regulation in prokaryotes. SignificanceThe evolution of multicellularity in bacteria involved the development of complex mechanisms to spatially and temporally coordinate cell division. Streptomyces, renowned for their production of bioactive secondary metabolites, exemplify bacterial complexity. This study reveals how Streptomyces employ the dynamin-like proteins DynAB as a bifunctional molecular switch, enabling transition between vegetative and reproductive growth through integrated interactions with developmentally regulated proteins and the availability of the energy supplier GTP. Importantly, DynAB could repress cell division in both Streptomyces and Escherichia coli, suggesting an evolutionary origin of these proteins prior to bacterial multicellularity. Our work reveals the dual function and switch mechanism of DynAB in Streptomyces, providing insights into the emergence of dynamic cell cycle control in prokaryotes.

microbiology↗

Neuronal SEL1L-HRD1 ERAD regulates one-carbon metabolism and is essential for motor function and survival

Hypomorphic variants in the SEL1L-HRD1 ER-associated degradation (ERAD) complex have been linked to severe neurological syndromes in children, including neurodevelopmental delay, intellectual disability, motor dysfunction, and early death. Despite this association, its physiological importance and underlying mechanisms in neurons remain poorly understood. Here, we show that neuronal SEL1L-HRD1 ERAD is essential for maintaining one-carbon metabolism, motor function, and overall viability. Neuron-specific deletion of Sel1L in mice (Sel1LSynCre) resulted in growth retardation, severe motor impairments, and early mortality by 9 weeks of age--mirroring core clinical features observed in affected patients--despite preserved neuronal numbers and only modest ER stress. Multi-omics analyses, including single-nucleus RNA sequencing and metabolomics, revealed significant dysregulation of one-carbon metabolism in ERAD-deficient brains. This included activation of the serine, folate, and methionine pathways, accompanied by elevated levels of S-adenosylmethionine and related metabolites, likely resulted from induction of the integrated stress response (ISR). Together, these findings uncover a previously unappreciated role for neuronal SEL1L-HRD1 ERAD in coordinating ER protein quality control with metabolic adaptation, providing new insight into the molecular basis of ERAD-related neurodevelopmental disease. SummaryUsing a neuron-specific Sel1L knockout mouse model, we demonstrate that Sel1L deficiency activates integrated stress responses, rewires one-carbon metabolism, and impairs motor function and survival.

cell biology↗

Pathogenicity and transmissibility of Monkeypox virus in dormice

The global spread of the monkeypox virus (MPXV) poses a significant challenge to public health, yet reliable and consistent animal models for evaluating MPXV remain limited, which to some extent restricts the advancement of treatment strategies and transmission-blocking technologies. As natural hosts, African dormice (Graphiurus spp.) represent promising candidates. However, the biological characteristics of MPXV in dormice remain largely unexplored. This study systematically evaluated the pathogenicity and transmissibility of MPXV in dormice. Experimental results demonstrated that dormice are highly susceptible to MPXV infection. Following intranasal inoculation, MPXV induced significant weight loss, lethal infections, and multi-organ pathological damage, with robust viral replication in respiratory and liver tissues. Notably, MPXV can efficiently transmit among dormice through direct contact, with one-third of the contact-exposed dormice shedding infectious viruses and two-thirds exhibiting seropositivity. In addition, one-third of the airborne exposure dormice show seropositivity, yet no infectious viruses were detected in their respiratory tissues, indicating that the airborne transmissibility of MPXV among dormice is relatively restricted. Furthermore, it was observed that infected dormice continuously released large quantities of virus-laden aerosols, with emissions peaking on 12 dpi (3.78{+/-}1.01x106 copies/dormouse/hour of respiration). Particle size analysis revealed that the viral copies in [≥]7 m coarse particles accounted for >90.9% of exhaled viral aerosols during peak shedding (8-14 dpi). These findings demonstrate that the African dormice serve as an effective animal model for assessing MPXV infection, pathogenicity, and transmission dynamics. Simultaneously, enhanced monitoring of wild dormouse populations is critical due to their potential role in MPXV transmission chains.

microbiology↗

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica, respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica. Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches.

genomics↗

Parameter Optimization for Iterative MINFLUX Microscopy enabled Single Particle Tracking

MINFLUX fluorescence microscopy is a recently introduced super-resolution approach for studying cellular structures and their dynamics with highest detail. Iterative MINFLUX (iMFX) performs Single Particle Tracking (SPT) at runtime. The ad hoc signal interpretation necessary to sustain the method relies on several parameters, which need to be optimized in relation to the sample under study, such as fluorescent lipid analogues in membranes, to ensure the fidelity of the measurement. We propose a parameter optimization strategy, an overview of the most important parameters, present a theoretical upper limit for trackable diffusion rates, and demonstrate iMFX-enabled SPT of fast ([<]DMSD[>] = 2.5m2/s) lateral Brownian motion of lipids in membranes.

biophysics↗

Dynamics of mesoscale brain network during decision-making learning revealed by chronic, large-scale single-unit recording

Associating unfamiliar stimuli with appropriate behavior through experience is crucial for survival. While task-relevant information was found to be distributed across multiple brain regions, how regional nodes in this distributed network reorganize their functional interactions throughout learning remains to be elucidated. Here, we performed chronic, large-scale single-unit recording across 10 cortical and subcortical regions using ultra-flexible microelectrode arrays in mice performing a visual decision-making task and tracked mesoscale functional network dynamics throughout learning. Task learning reshaped interregional functional connectivity, leading to the emergence of a subnetwork involving visual and frontal regions during the acquisition of correct No-Go responses. This reorganization was accompanied by a more widespread representation of visual stimulus across regions, and a regions network rank strongly predicted its peak timing of visual information encoding. Together, our findings revealed that mesoscale networks undergo dynamic restructuring during learning, with functional connectivity ranks influencing the propagation of sensory information across the network.

neuroscience↗

Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis

The benign-to-malignant transition is a defining step in cancer progression. To investigate when and how malignancy initiation occurs and tissue reorganization proceeds, we combine single-cell and spatial transcriptomic profiling in mouse models of pancreatic ductal adenocarcinoma (PDAC) that capture spontaneous p53 loss. Among Kras-mutant cells, we find that oncogenic and tumor-suppressive programs, including those controlled by p53, CDKN2A, and SMAD4, are co-activated in a discrete progenitor-like population, engaging senescence-like responses. Using a framework we develop for spatial analysis, we show that a niche centered on these cells undergoes stepwise remodeling during tumor progression, mirroring invasive PDAC. Transient KRAS inhibition depletes progenitor-like cells and dismantles their niche, delaying malignancy initiation. Conversely, p53 suppression enables progenitor cell expansion, epithelial-mesenchymal reprogramming, and immune-privileged niche formation. These findings position the progenitor-like state at the convergence of cancer-driving mutations, plasticity and tissue remodeling, revealing a critical window for intercepting malignancy.

cancer biology↗

Inhibiting RhoA Activation via GDP-state Stabilization to Relieve Heart Failure

High rates of heart failure (HF) morbidity and mortality have made targeting myocardial remodeling--particularly hypertrophy and fibrosis--a key therapeutic focus. RhoA, which regulates cytoskeletal reorganization and cell migration, plays a role in this process. However, RhoA has long been considered "undruggable", due to its strong binding to its endogenous substrates, GDP/GTP, and the lack of well-defined pockets for drug targeting. Here, we discovered a cryptic pocket proximate to GDP within RhoA and identified a natural product, AH001, binds here and interacts with GDP, stabilizing RhoAs interaction with its endogenous inhibitor, RhoGDI. AH001 reduced the downstream MRTFA nuclear translocation and downregulated fibrosis/hypertrophy proteins. Consequently, AH001 mitigated myocardial remodeling in multiple HF animal models, and in the 3D myocardial tissue model. Our findings highlight the therapeutic potential of inhibiting RhoA activation in myocardial remodeling, ultimately targeting HF, and offer a promising avenue for developing reversible inhibitors against undruggable GTPases.

pharmacology and toxicology↗

Contrastive Learning-Enhanced Drug Metabolite Prediction Drives the Discovery of an Orally Bioavailable RSK4 Inhibitor for Esophageal Cancer

Drug metabolism liabilities are a major bottleneck in drug development, necessitating accurate metabolite prediction tools. While AI-driven methods have advanced, challenges remain in achieving high-precision, robustness, broad reaction coverage and seamless integration into the drug development workflow. To address this, we first constructed the most comprehensive human-specific drug metabolism database to date, encompassing 11,665 human metabolic reactions and 2,497 high-quality rules. Leveraging this resource, we developed ConMeter (Contrastive learning and feature interaction based Metabolic Reaction prediction), a novel model integrating chemical feature interaction and contrastive learning. ConMeter demonstrates significant improvements, achieving [~]80% accuracy in identifying at least one metabolite within the top 5 predictions and showing an average 25% relative enhancement in ranking true positives compared to state-of-the-art methods. The comprehensive database also expands the range of predictable metabolic reactions. To demonstrate the utility of ConMeter, we integrated it into a metabolite prediction-guided drug design strategy aimed at addressing the low oral bioavailability of a metabolically vulnerable RSK4 lead compound -- a pervasive issue among known RSK inhibitors. This strategy successfully yielded R636, a novel RSK4 inhibitor exhibiting remarkably improved bioavailability (a 63-fold increase, reaching 63% absolute bioavailability) while maintaining its potent activity. Notably, R636 showed favorable safety profile and significant anti-tumor efficacy against esophageal squamous cell carcinoma (ESCC) in vitro and in two distinct patient-derived xenograft (PDX) mouse models. This work introduces ConMeter as a powerful and practical tool for high-accuracy metabolite prediction, demonstrating its potential to accelerate lead optimization, exemplified by the discovery of R636 as a promising orally bioavailable candidate for ESCC.

cancer biology↗