Biology subjects

Bai, F.

Publications and source records attributed to Bai, F..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Bacterial stress granule protects mRNA through ribonucleases exclusion

Membraneless droplets formed through liquid-liquid phase separation of ribonucleoprotein particles contribute to mRNA storage in eukaryotic cells. How such aggresomes contribute to mRNA dynamics under stress, and their functional role, is less understood in bacteria. Here we used multiple approaches including live-cell imaging, polymer physics modelling and transcriptomics to show that prolonged stress leading to ATP depletion in Escherichia coli results in increased aggresome formation, compaction, and selective mRNA enrichment within these aggresomes. Longer transcripts accumulate more in aggresomes than in the cytosol. Mass spectrometry and mutagenesis studies showed that mRNA ribonucleases are excluded from aggresomes due to electrostatic repulsion arising from their negative surface charges. Experiments with fluorescent reporters and disruption of aggresome formation showed that mRNA storage within aggresomes promoted rapid translation reactivation and associated with reduced lag phases during growth after stress removal. Our findings suggest that mRNA storage within aggresomes confers an advantage for bacterial survival and recovery from stress.

biophysics↗

bioRxiv2024

Thymidine Phosphorylase Mediates SARS-CoV-2 Spike Protein Enhanced Thrombosis in K18-hACE2TG Mice

COVID-19, caused by SARS-CoV-2, is associated with arterial and venous thrombosis, thereby increasing mortality. SARS-CoV-2 spike protein (SP), a viral envelope structural protein, is implicated in COVID-19-associated thrombosis. However, the underlying mechanisms remain unknown. Thymidine phosphorylase (TYMP), a newly identified prothrombotic protein, is upregulated in the plasma, platelets, and lungs of patients with COVID-19 but its role in COVID-19-associated thrombosis is not defined. In this study, we found that wild-type SARS-CoV-2 SP significantly promoted arterial thrombosis in K18-hACE2TG mice. SP-accelerated thrombosis was attenuated by inhibition or genetic ablation of TYMP. SP increased the expression of TYMP, resulting in the activation of signal transducer and activator of transcription 3 (STAT3) in BEAS-2B cells, a human bronchial epithelial cell line. A siRNA-mediated knockdown of TYMP inhibited SP-enhanced activation of STAT3. Platelets derived from SP-treated K18-hACE2TG mice also showed increased STAT3 activation, which was reduced by TYMP deficiency. Activated STAT3 is known to potentiate glycoprotein VI signaling in platelets. While SP did not influence ADP- or collagen-induced platelet aggregation, it significantly shortened activated partial thromboplastin time and this change was reversed by TYMP knockout. Additionally, platelet factor 4 (PF4) interacts with SP, which also complexes with TYMP. TYMP enhanced the formation of the SP/PF4 complex, which may potentially augment the prothrombotic and procoagulant effects of PF4. We conclude that SP upregulates TYMP expression, and TYMP inhibition or knockout mitigates SP-enhanced thrombosis. These findings indicate that inhibition of TYMP may be a novel therapeutic strategy for COVID-19-associated thrombosis. Key PointsO_LISARS-CoV-2 spike protein, thymidine phosphorylase, and platelet factor 4 form a complex that may promote clot formation. C_LIO_LIInhibiting thymidine phosphorylase attenuates SARS-CoV-2 spike protein-enhanced thrombosis, platelet activation, and coagulation. C_LI

cell biology↗

bioRxiv2024

Pre-existing Immunity to Influenza Aids Ferrets in Developing Stronger and Broader Vaccine-induced Antibody Responses

Influenza seasons occur annually, building immune history for individuals, but the influence of this history on subsequent influenza vaccine protection remains unclear. We extracted data from an animal trial to study its potential impact. The trial involved 80 ferrets, each receiving either one type of infection or a placebo before vaccination. We quantified the vaccine protection by evaluating hemagglutination inhibition (HAI) antibody titer responses. We tested whether hosts with different infection histories exhibited similar level of responses when receiving the same vaccine for all homologous and heterologous outcomes. We observed that different pre-existing immunities were generally beneficial to vaccine induced responses, but varied in magnitude. Without pre-immunity, post-vaccination HAI titers after the 1st dose of the vaccine were less likely to be above 1:40, and a booster shot was needed. Our study suggests that pre-existing immunity may strengthen and extend the homologous and heterologous vaccine protection.

immunology↗

bioRxiv2023

Conformational Space Profile Enhances Generic Molecular Representation Learning

The molecular representation model is a neural network that converts molecular representations (SMILES, Graph) into feature vectors, that carries the potential to be applied across a wide scope of drug discovery scenarios. However, current molecular representation models have been limited to 2D or static 3D structures, overlooking the dynamic nature of small molecules in solution and their ability to adopt flexible conformational changes crucial for drug-target interactions. To address this limitation, we propose a novel strategy that incorporates the conformational space profile into molecular representation learning. By capturing the intricate interplay between molecular structure and conformational space, our strategy enhances the representational capacity of our model named GeminiMol. Consequently, when pre-trained on a miniaturized molecular dataset, the GeminiMol model demonstrates a balanced and superior performance not only on traditional molecular property prediction tasks but also on zero-shot learning tasks, including virtual screening and target identification. By capturing the dynamic behavior of small molecules, our strategy paves the way for rapid exploration of chemical space, facilitating the transformation of drug design paradigms.

bioinformatics↗

bioRxiv2023

USP7 Inhibition Promotes Mesenchymal Stem cell-Macrophage Crosstalk in Age-related Osteoporosis via Efferocytosis and Senolysis

Although elderly osteoporotic patients have similar implant survival rates compared to those of normal individuals, they require longer healing periods to achieve proper osseointegration. This may be related to chronic inflammatory responses and impaired stem cell repair functions in the osteoporotic bone microenvironment. Recently, the deubiquitinating enzyme, ubiquitin-specific peptidase 7 (USP7), was found to regulate macrophage immune response and modulate stem cell osteogenic differentiation. The selective inhibitor of USP7, P5091, has also been found to promote bone repair and homeostasis in osteoporotic conditions. However, the roles of USP7 and P5091 in osteoimmunology and dental implant osseointegration under senile osteoporotic conditions remain unclear. In this study, USP7 depletion and P5091 were showed to inhibit inflammation in senescent bone marrow derived macrophages (BMDMs) and promote osteogenic differentiation in aged BMSCs. Furthermore, mRNA-Seq revealed that USP7 depletion could enhance efferocytosis in senescent BMDMs through the EPSIN1/ low-density lipoprotein receptor-related protein 1 (LRP1) pathway and selectively induce apoptosis (senolysis) in aged BMSCs. In senile osteoporotic mice, we found that the osseointegration period was prolonged compared to young mice, and P5091 promoted the early stage of osseointegration, which may be related to macrophage efferocytosis around the implant. Collectively, this study suggests that USP7 inhibition may accelerate the osseointegration process in senile osteoporotic conditions by promoting macrophage efferocytosis and aged BMSCs apoptosis. This has implications for understanding the cellular interactions and signaling mechanisms in the peri-implant bone microenvironment under osteoporotic conditions. It may also provide clinical significance in developing new therapies to enhance osseointegration quality and shorten the edentulous period in elderly osteoporotic patients.

cell biology↗

bioRxiv2023

Cutaneous T cell lymphoma atlas reveals malignant Th2 cells supported by a B cell-rich microenvironment

Cutaneous T-cell lymphoma (CTCL) is a potentially fatal clonal malignancy of T cells primarily affecting the skin. The most common form of CTCL, mycosis fungoides (MF), can be difficult to diagnose resulting in treatment delay. The pathogenesis of CTCL is not fully understood due to limited data from patient studies. We performed single-cell RNA sequencing and spatial transcriptomics profiling of skin from patients with MF-type CTCL, and an integrated comparative analysis with human skin cell atlas datasets from healthy skin, atopic dermatitis and psoriasis. We reveal the co-optation of Th2-immune gene programmes by malignant CTCL cells and modelling of the tumour microenvironment to support their survival. We identify MHC-II+ fibroblast subsets reminiscent of lymph node T-zone reticular cells and monocyte-derived dendritic cells that can maintain Th2-like tumour cells. CTCL Th2-like tumour cells are spatially associated with B cells, forming aggregates reminiscent of tertiary lymphoid structures which are more prominent with progressive disease. Finally, we validated the enrichment of B cells in CTCL skin infiltrates and its association with disease progression across three independent patient cohorts. Our findings provide diagnostic aids, potential biomarkers for disease staging and therapeutic strategies for CTCL.

genomics↗

bioRxiv2022

A non-human primate model with Alzheimer's disease-like pathology induced by hippocampal overexpression of human tau

Alzheimers disease (AD) is one of the most burdening diseases of the century with no disease-modifying treatment yet. Non-human primates (NHPs) share genetic, anatomical and physiological similarities with humans, making them an ideal model for investigating the pathogenesis and therapeutics of AD. However, the applications of NHPs in AD research have been hindered by the paucity of spontaneous or induced monkey models for AD due to their long generation time, ethical considerations and technical challenges in making genetically modified monkeys. Here we developed an AD-like NHP model by overexpressing human tau in bilateral hippocampi of adult rhesus macaque monkeys. We evaluated the pathological features of these monkeys with immunostaining, cerebrospinal fluid (CSF) analysis, magnetic resonance imaging (MRI), positron emission tomography (PET) scan, and behavioral tests. We demonstrated that after hippocampal overexpression of human tau, the rhesus macaque monkeys displayed multiple pathological features of AD, including neurofibrillary tangle formation, neuronal loss, hippocampal atrophy, neuroinflammation, A{beta} clearance deficit, blood vessel damage and cognitive decline. This work establishes a human tau-induced AD-like NHP model that may facilitate mechanistic studies and therapeutic treatments for AD.

neuroscience↗

bioRxiv2022

Sensitive bacterial Vm sensors revealed the excitability of bacterial Vm and its role in antibiotic tolerance

As an important free energy source, the membrane voltage (Vm) regulates many essential physiological processes in bacteria. However, in comparison with eukaryotic cells, knowledge of bacterial electrophysiology is very limited. Here, we developed a set of novel genetically encoded bacterial Vm sensors which allow single-cell recording of bacterial Vm dynamics in live cells with high temporal resolution. Using these new sensors, we reveal the electrically "excitable" and "resting" states of bacterial cells dependent on their metabolic status. In the electrically excitable state, frequent hyperpolarization spikes in bacterial Vm are observed, which facilitates increased antibiotic tolerance. In the electrically resting state, bacterial Vm displays significant cell-to-cell heterogeneity and is linked to the cell fate after antibiotic treatment.

microbiology↗

bioRxiv2022

Selection and validation of reference genes for quantitative real-time polymerase chain reaction in Serratia ureilytica DW2

Serratia ureilytica DW2 is a highly efficient phosphate-solubilizing bacterium isolated from Codonopsis pilosula rhizosphere soil that can promote the growth of C. pilosula. However, no validated reference genes from the genus Serratia for use in quantitative real-time polymerase chain reaction (RT-qPCR) normalization have been reported. To screen stable reference genes in S. ureilytica DW2, the expression of eight candidate reference genes (16S rRNA, ftsZ, ftsA, mreB, recA, slyD, thiC, and zipA) under different treatment conditions (pH, temperature, culture time, and salt content) was assayed by RT-qPCR. The expression stability of these genes was analyzed with different algorithms (geNorm, NormFinder, and BestKeeper). To verify the reliability of the data, the most stably expressed reference gene was used to quantify expression of the glucose dehydrogenase (gdh) gene under different soluble phosphate levels. The results showed that the zipA and 16S rRNA genes were the most stable reference genes, and the least stable were thiC and recA. The expression of gdh was consistent with the phosphate solubilization ability on plates containing National Botanical Research Institute phosphate (NBRIP) growth medium. Therefore, this study provides a stable and reliable reference gene for Serratia, which is vital for the accurate quantification of functional gene expression in future studies.

microbiology↗

bioRxiv2022

A complete MAPK cascade, a calmodulin, and a protein phosphatase act downstream of CRK receptor kinases and regulate Arabidopsis innate immunity

Mitogen-activated protein kinase (MAPK) cascades are critical signal transduction modules in stress responses, but how their composition and mode of activation induces a stress response is poorly understood. We showed in Arabidopsis that CRK21, a cysteine-rich receptor-like protein kinase (CRK), phosphorylates MAPK kinase kinase 20 (MKKK20) and thus directly activates a novel MAPK cascade, consisting of MKKK20, the MAPK kinase MKK3, and the MAPK MPK6. Furthermore, the protein phosphatase PP2C76 and the calmodulin CaM7 were identified as negative and positive modulators of the cascade, respectively. Loss-of-function in components of the MAPK cascade or in CaM7 led to susceptibility to the bacterial pathogen Pseudomonas syringae and the fungal pathogen Botrytis cinerea. In contrast, loss-of-function of PP2C76 as well as transient overexpression of the genes in the MAPK cascade and CaM7 conferred resistance to the pathogens. Moreover, seven additional CRKs interacted with MKKK20 in vivo, and four of these were highly expressed after inoculation with P. syringae. In summary, our findings demonstrate that the novel CRK21-MKKK20-MKK3-MPK6 signaling pathway functions in immunity to fungal and bacterial pathogens and that CRKs may function in directly activating MKKKs.

plant biology↗

bioRxiv2022

Structural insights as to how iron-loaded siderophores are imported into Mycobacterium tuberculosis by IrtAB

The ATP-binding cassette (ABC) transporter, IrtAB, plays a vital role in the replication and viability of Mycobacterium tuberculosis (Mtb), where its function is to import iron-loaded siderophores. Unusually, it adopts the typical fold of canonical ABC exporters. Here, we report the structure of unliganded Mtb IrtAB and its structure in complex with ATP, ADP, and an ATP analogue (AMP-PNP) at resolutions from 2.9 to 3.5 [A]. In the ATP-bound state, the two nucleotide-binding domains (NBDs) form a "head-to-tail" dimer, but IrtAB has an unexpectedly occluded conformation, with the inner core forming a large hydrophilic cavity of about 4600 [A]3. Comparison of the structure of the transporter in inward-facing and occluded conformations reveals that the NBD and the intracellular helical region of transmembrane domain (TMD) have an asymmetric allosteric mechanism when ATP binding/hydrolysis such that the one exhibits rigid-body rotation and the other moves in a concerted response as a rigid body. This study provides a molecular basis for the ATP-driven conformational changes that occur in IrtAB and an explanation as to how iron-loaded siderophores are imported into Mtb by IrtAB.

molecular biology↗

bioRxiv2021

Neural encoding of phrases and sentences in spoken language comprehension

Speech stands out in the natural world as a biological signal that communicates formally-specifiable complex meanings. However, the acoustic and physical dynamics of speech do not injectively mark the linguistic structure and meaning that we perceive. Linguistic structure must therefore be inferred through the human brains endogenous mechanisms, which remain poorly understood. Using electroencephalography, we investigated the neural response to synthesized spoken phrases and sentences that were closely physically-matched but differed in syntactic structure, under either linguistic or non-linguistic task conditions. Differences in syntactic structure were well-captured in theta band ([~] 2 to 7 Hz) phase coherence, phase connectivity degree at low frequencies (< [~] 2 Hz), and in both intensity and degree of power connectivity of induced neural response in the alpha band ([~] 7.5 to 13.5 Hz). Theta-gamma phase-amplitude coupling was found when participants listened to speech, but it did not discriminate between syntactic structures. Spectral-temporal response function modelling suggested different encoding states in both temporal and spectral dimensions as a function of the amount and type of linguistic structure perceived, over and above the acoustically-driven neural response. Our findings provide a comprehensive description of how the brain separates linguistic structures in the dynamics of neural responses, and imply that phase synchronization and strength of connectivity can be used as readouts for constituent structure, providing a novel basis for future neurophysiological research on linguistic structure in the brain.

neuroscience↗

bioRxiv2021

A spatial and cellular distribution of neurotropic virus infection in the mouse brain revealed by fMOST and single cell RNA-seq

Neurotropic virus infection can cause serious damage to the central nervous system (CNS) in both human and animals. The complexity of the CNS poses unique challenges to investigate the infection of these viruses in the brain using traditional techniques. In this study, we explore the use of fluorescence micro-optical sectioning tomography (fMOST) and single cell RNA sequencing (scRNA-seq) to map the spatial and cellular distribution of a representative neurotropic virus, rabies virus (RABV), in the whole brain. Mice were inoculated with a lethal dose of recombinant RABV expressing enhanced green fluorescent protein (EGFP) under different infection routes, and a three-dimensional view of the distribution of RABV in the whole mouse brain was obtained using fMOST. Meanwhile, we pinpointed the cellular distribution of RABV by utilizing scRNA-seq. Our fMOST data provide the first evidence that RABV can infect multiple nuclei related to fear independent of different infection routes. More surprisingly, scRNA-seq data indicate that besides neurons RABV can infect macrophages and NK cells in vivo. Collectively, this study draws a comprehensively spatial and cellular map of RABV infection in the mouse brain, providing a novel and insightful strategy to investigate the pathogenesis of neurotropic viruses.

microbiology↗

bioRxiv2021

A chloride efflux transporter OsBIRG1 regulates grain size and salt tolerance in rice

Grain size is determined by the number of cells and cell size of the grain. Regulation of grain size is crucial for improving crop yield. However, the genes and underlying molecular mechanisms controlling grain size remain elusive. Here we report a member of Detoxification efflux carrier (DTX)/Multidrug and Toxic Compound Extrusion (MATE) family transporter, BIG RICE GRAIN 1 (BIRG1), negatively regulates the grain size in rice. BIRG1 is highly expressed in reproductive organs and roots. In birg1 grain, the size of the outer parenchyma layer cells of spikelet hulls is noticeably larger but the cell number is not altered compared with that in the wild-type (WT) grain. When expressed in Xenopus oocytes, BIRG1 exhibits chloride efflux activity. In line with the role of BIRG1 in mediating chloride efflux, the birg1 mutant shows reduced tolerance to salt stress under which the chloride level is toxic. Moreover, the birg1 grains contain higher level of chloride compared to WT grains when grown under normal paddy field. The birg1 roots accumulate more chloride than those of WT under saline condition. Collectively, our findings suggest that BIRG1 functions as a chloride efflux transporter regulating grain size and salt tolerance via controlling chloride homeostasis in rice.

plant biology↗

bioRxiv2020

A body map of somatic mutagenesis in morphologically normal human tissues

Somatic mutations accumulated in normal tissues are associated with aging and disease. Here, we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies (~ 600 cells each), mostly from the epithelia, of nine organs from five donors. We found that somatic mutation accumulations and clonal expansions are widespread, although with variable extent, in morphologically normal human tissues. Somatic copy number alterations were rarely detected, except for tissues from esophagus and cardia. Endogenous mutational processes like SBS1 and SBS5 are ubiquitous among normal tissues though exhibiting different relative activities. Exogenous mutational processes like SBS22 were found in different tissues from the same donor. We reconstructed the spatial somatic clonal architecture with sub-millimeter resolution. In epithelial tissues from esophagus and cardia, macroscopic somatic clones expanded to several millimeters were frequently seen, whereas in tissues from colon, rectum, and duodenum somatic clones were microscopic in size and evolved independently. Our study depicted a body map of somatic mutations and clonal expansions from the same individuals, and it revealed that the degree of somatic clonal expansion and enrichment of driver mutations are highly organ specific.

genomics↗

bioRxiv2020

Single-cell landscape of immunological responses in COVID-19 patients

In COVID-19 caused by SARS-CoV-2 infection, the relationship between disease severity and the host immune response is not fully understood. Here we performed single-cell RNA sequencing in peripheral blood samples of five healthy donors and 13 COVID-19 patients including moderate, severe and convalescent cases. Through determining the transcriptional profiles of immune cells, coupled with assembled T cell receptor and B cell receptor sequences, we analyzed the functional properties of immune cells. Most cell types in COVID-19 patients showed a strong interferon-alpha response, and an overall acute inflammatory response. Moreover, intensive expansion of highly cytotoxic effector T cell subsets, such as CD4+ Effector-GNLY (Granulysin), CD8+ Effector-GNLY and NKT CD160, was associated with convalescence in moderate patients. In severe patients, the immune landscape featured a deranged interferon response, profound immune exhaustion with skewed T cell receptor repertoire and broad T cell expansion. These findings illustrate the dynamic nature of immune responses during the disease progression.

immunology↗

bioRxiv2020

The prevalence of Angiostrongylus cantonensis in rodent hosts in China and several Asian countries: a systematic review and meta-analysis

BackgroundAngiostrogylus cantonensis (A.cantonensis) is a zoonotic parasitic nematode, with a worldwide distribution, causing eosinophilic meningitis or meningoencephalitis in humans. Although the biology of A.cantonensis is relatively well known, little is understood about the transmission level in different zoogeographical regions, especially in Asia. Here, to evaluate the prevalence of A.cantonensis in rodent hosts in China and several Asian countries, we conducted a systematic review registered with PROSPERO (CRD42020161665). MethodsRecords were selected systematically from 7 databases (Medline via to Pubmed, Web of science, Scopus, Google Scholar, CNKI, Wangfang, CBM). Forest plots and random-effects model were used to display pooled estimates. The Freeman-Tukey double arcsine transformation of R software was used to conduct meta-analysis and statistical significance was set at 0.05. ResultsA total of 67 studies met the inclusion criteria and were included in the systematic review and meta-analysis. The pooled prevalence estimates of A.cantonensis infection in rodents was 0.1003 (95%CI: 0.0765, 0.1268). There was significant heterogeneity in reported outcomes (p<0.0001). So we considered that there was no publication bias in the included studies. ConclusionThe A.cantonensis infection rate among rodent hosts was still high in Asia, particularly in China, especially in Rattus norvegicus, and thus comprehensive measures should be taken for rodent hosts control to avoid an angiostrongyliasis outbreak. Due to the wide distribution and movement of rodent hosts, people in all regions of China, even in other Asia area live at risk of an infection. Hence, the development of more reliable diagnostic tests will be key for an effective identification of cases as well as improved patient care. Consequently, further studies are required to updated strategies for controlling A.cantonensis infection among human population.

molecular biology↗

bioRxiv2020

Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p

Clinical use of antimicrobials faces great challenges from the emergence of multidrug resistant (MDR) pathogens. The overexpression of drug efflux pumps is one of the major contributors to MDR. It is considered as a promising approach to overcome MDR by reversing the function of drug efflux pumps. In the life-threatening fungal pathogen Candida albicans, the major facilitator superfamily (MFS) transporter Mdr1p can excrete many structurally unrelated antifungals, leading to multidrug resistance. Here we report a counterintuitive case of reversing multidrug resistance in C. albicans by using a natural product berberine to hijack the overexpressed Mdr1p for its own importation. Moreover, we illustrate that the imported berberine accumulates in mitochondria, and compromises the mitochondrial function by impairing mitochondrial membrane potential and mitochondrial Complex I. It results in the selective elimination of Mdr1p overexpressed C. albicans cells. Furthermore, we show that berberine treatment can prolong the mean survival time (MST) of mice with a blood-borne dissemination of Mdr1p overexpressed multidrug resistant candidiasis. This study provided a potential direction of novel anti-MDR drug discovery by screening for multidrug efflux pump converters.

microbiology↗