Biology subjects

Liu, N.

Publications and source records attributed to Liu, N..

At least 145 records · Page 8Linked to original sources

bioRxiv2021

A pair of transporters controls mitochondrial Zn2+ levels to maintain mitochondrial homeostasis

Zn2+ is required for the activity of many mitochondrial proteins, which regulate mitochondrial dynamics, apoptosis and mitophagy. However, it is not understood how the proper mitochondrial Zn2+ level is achieved to maintain mitochondrial homeostasis. Using Caenorhabditis elegans, we reveal here that a pair of mitochondrion-localized transporters controls the mitochondrial level of Zn2+. We demonstrate that SLC-30A9/ZnT9 is a mitochondrial Zn2+ exporter. Loss of SLC-30A9 leads to mitochondrial Zn2+ accumulation, which damages mitochondria, impairs animal development and shortens the life span. We further identify SLC-25A25/SCaMC-2 as an important regulator of mitochondrial Zn2+ import. Loss of SLC-25A25 suppresses the abnormal mitochondrial Zn2+ accumulation and defective mitochondrial structure and functions caused by loss of SLC-30A9. Moreover, we reveal that the endoplasmic reticulum contains the Zn2+ pool from which mitochondrial Zn2+ is imported. These findings establish the molecular basis for controlling the correct mitochondrial Zn2+ levels for normal mitochondrial structure and functions. SummaryZn2+ is a trace ion essential for the function of many mitochondrial proteins. It is not known how mitochondrial Zn2+ levels are regulated. Ma at al. identify transporters that mediate mitochondrial Zn2+ export and import to maintain mitochondrial homeostasis.

cell biology↗

bioRxiv2021

Perfluorononanoic acid impedes mouse oocyte maturation by inducing mitochondrial dysfunction and oxidative stress

Perfluorononanoic acid (PFNA), a member of PFAS, is frequently detected in human blood and tissues, even in follicular fluid of women. The exposure of PFNA, but not PFOA and PFOS, is positively correlated with miscarriage and increased time to pregnancy. Toxicological studies indicated that PFNA exposure is associated with immunotoxicity, hepatotoxicity, developmental toxicity, and reproductive toxicity in animals. However, there is little information regarding the toxic effects of PFNA on oocyte maturation. In this study, we investigated the toxic effects of PFNA exposure on mouse oocyte maturation in vitro. Our results showed that 600 M PFNA significantly inhibited germinal vesicle breakdown (GVBD) and polar body extrusion (PBE) in mouse oocytes. Our further study revealed that PFNA induced abnormal metaphase I (MI) spindle assembly, evidenced by malformed spindles and mislocalization of p-ERK1/2 in PFNA-treated oocytes. We also found that PFNA induced abnormal mitochondrial distribution and increased mitochondrial membrane potential. Consequently, PFNA increased reactive oxygen species (ROS) levels, leading to oxidative stress, DNA damage, and eventually early-stage apoptosis in oocytes. In addition, after 14 h culture, PFNA disrupted the formation of metaphase II (MII) spindle in most PFNA-treated oocytes with polar bodies. Collectively, our results indicate that PFNA interferes with oocyte maturation in vitro via disrupting spindle assembly, damaging mitochondrial functions, and inducing oxidative stress, DNA damage, and early-stage apoptosis.

cell biology↗

bioRxiv2021

MAGI2-AS3 modulates proliferation, apoptosis and glycolysis in acute lymphoblastic leukemia via miR-452-5p/FOXN3 axis

BackgroundLong non-coding RNA MAGI2 antisense RNA 3 (MAGI2-AS3) has been identified as a tumor suppressor in various cancers. Acute lymphoblastic leukemia (ALL) is a prevalent kind of leukemia among children. In this study, we aimed at evaluate the role of MAGI2-AS3 in ALL and its underlying mechanisms. MethodsqPCR was adopted to determine MAGI2-AS3, miR-452-5p, and FOXN3 expression. The malignant properties of ALL cells were assessed by CCK8 assay and flow cytometry analysis. The glucose uptake, lactate production, and ATP level were measured to evaluate glycolysis. Western blotting was performed to detect PCNA, Bcl-2, Bax, and HK2 protein levels. The interaction between MAGI2-AS3/FOXN3 and miR-452-5p was validated by luciferase reporter assay. The in vivo growth of ALL cells was determined in xenograft model. ResultsMAGI2-AS3 was strikingly down-regulated in ALL samples and cells. Overexpression of MAGI2-AS3 restrained growth, glycolysis and triggered apoptosis of ALL cells. Mechanistically, MAGI2-AS3 could sponge miR-452-5p to up-regulate FOXN3. Silencing of FOXN3 abolished the anti-tumor effect of MAGI2-AS3. Finally, MAGI2-AS3 suppressed the in vivo growth of ALL cells via modulating miR-452-5p/FOXN3 axis. ConclusionOur findings demonstrate that MAGI2-AS3 delays the progression of ALL by regulating miR-452-5p/FOXN3 signaling pathway.

cancer biology↗

bioRxiv2021

Structure and computation-guided design of a mutation-integrated trimeric RBD candidate vaccine with broad neutralization against SARS-CoV-2

The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 is an attractive target for COVID-19 vaccine developments, which naturally exists in a trimeric form. Here, guided by structural and computational analyses, we present a mutation-integrated trimeric form of RBD (mutI tri-RBD) as a broadly protective vaccine candidate, in which three RBDs were individually grafted from three different circulating SARS-CoV-2 strains including the prototype, Beta (B.1.351) and Kappa (B.1.617). The three RBDs were then connected end-to-end and co-assembled to possibly mimic the native trimeric arrangements in the natural S protein trimer. The recombinant expression of the mutI tri-RBD, as well as the homo-tri-RBD where the three RBDs were all truncated from the prototype strain, by mammalian cell exhibited correct folding, strong bio-activities, and high stability. The immunization of both the mutI tri-RBD and homo-tri-RBD plus aluminum adjuvant induced high levels of specific IgG and neutralizing antibodies against the SARS-CoV-2 prototype strain in mice. Notably, regarding to the "immune-escape" Beta (B.1.351) variant, mutI tri-RBD elicited significantly higher neutralizing antibody titers than homo-tri-RBD. Furthermore, due to harboring the immune-resistant mutations as well as the evolutionarily convergent hotspots, the designed mutI tri-RBD also induced strong broadly neutralizing activities against various SARS-CoV-2 variants, especially the variants partially resistant to homo-tri-RBD. Homo-tri-RBD has been approved by the China National Medical Products Administration to enter clinical trial (No. NCT04869592), and the superior broad neutralization performances against SARS-CoV-2 support the mutI tri-RBD as a more promising vaccine candidate for further clinical developments.

immunology↗

bioRxiv2021

Genetic characteristics of human papillomavirus type 16, 18, 52 and 58 in southern China

Persistent infections of high-risk human papillomaviruses (HPVs) are the leading cause of cervical cancers. We collected cervical exfoliated cell samples from females in Changsha city, Hunan Province and obtained 358 viral genomes of four major HPV types, including HPV 16 (n=82), 18 (n=35), 52 (n=121) and 58 (n=100). The lineage/sublineage distribution of the four HPVs confirmed previous epidemiological reports, with the predominant prevailing sublineage as A4 (50%), A1 (37%) and A3 (13%) for HPV16, A1 (83%) for HPV18, B2 (86%) for HPV52 and A1 (65%), A3 (19%) and A2 (12%) for HPV58. We also identified two potentially novel HPV18 sublineages, i.e. A6 and A7. Virus mutation analysis further revealed the presence of HPV16 and HPV58 strains associated with potentially high oncogenicity. These findings expanded our knowledge on the HPV genetic diversity in China, providing valuable evidence to facilitate HPV DNA screening, vaccine effectiveness evaluation and control strategy development.

genomics↗

bioRxiv2021

Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM

Although single-particle cryogenic electron microscopy (cryo-EM) has been applied extensively for elucidating many crucial biological mechanisms at the molecular level, this technique still faces critical challenges, the major one of which is to prepare the high-quality cryo-EM specimen. Aiming to achieve a more reproducible and efficient cryo-EM specimen preparation, novel supporting films including graphene-based two-dimensional materials have been explored in recent years. Here we report a robust and simple method to fabricate EM grids coated with single- or few-layer reduced graphene oxide (RGO) membrane in large batch for high-resolution cryo-EM structural determination. The RGO membrane has decreased interlayer space and enhanced electrical conductivity in comparison to regular graphene oxide (GO) membrane. Moreover, we found that the RGO supporting film exhibited nice particle-absorption ability, thus avoiding the air-water interface problem. More importantly, we found that the RGO supporting film is particularly useful in cryo-EM reconstruction of sub-100 kDa biomolecules at near-atomic resolution, as exemplified by the study of RBD-ACE2 complex and other small protein molecules. We envision that the RGO membranes can be used as a robust graphene-based supporting film in cryo-EM specimen preparation.

biophysics↗

bioRxiv2021

Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta

Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA barcoding to compare bacterial species composition at seedling, vegetative, early-, and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on non-serpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.

microbiology↗

bioRxiv2021

Thinopyrum intermedium TiAP1 interacts with a chitin deacetylase from Blumeria graminis f. sp. tritici and increases the resistance to Bgt in wheat

The biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt) is a crucial factor causing reduction of global wheat production. Wild wheat relatives, e.g. Thinopyrum intermedium, is one of the wild-used parents in wheat disease-resistant breeding. From T. intermedium line, we identified the aspartic acid protein gene, TiAP1, which involved in resistance against Bgt. TiAP1 is a secreted protein that accumulates in large amounts at the infection sites of powdery mildew and extends to the intercellular space. Yeast two-hybrid showed that it interacted with the chitin deacetylase (BgtCDA1) of Bgt. The yeast expression, purification, and invitro test confirmed the chitin deacetylase activity of BgtCDA1. The bombardment and VIGS mediated host-induced gene silencing showed BgtCDA1 promotes the invasion of Bgt. Transcriptome analysis showed the cell wall xylan metabolism, lignin biosynthesis-related, and defence genes involved in the signal transduction were upregulated in the transgenic TiAP1 wheat induced by Bgt. The TiAP1 in wheat may inactivate the deacetylation function of BgtCDA1, cause chitin oligomers expose to wheat chitin receptor, then trigger the wheat immune response to inhibit the growth and penetration of Bgt, and thereby enhance the tolerance of wheat to pathogens.

plant biology↗

bioRxiv2021

BRD2 inhibition blocks SARS-CoV-2 infection in vitro by reducing transcription of the host cell receptor ACE2

SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. We found that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a novel therapeutic target for COVID-19.

cell biology↗

bioRxiv2021

Incidence and Characteristics of Co-infection and Secondary Infection in Patients with COVID-19

ObjectiveThe etiology and epidemiology of co-infection and secondary infection in COVID-19 patients remain unknown. The study aims to investigate the occurrence and characteristics of co-infection and secondary infection in COVID-19 patients, mainly focusing on Streptococcus pneumoniae co-infections. MethodsThis study was a prospective, observational cohort study of the inpatients diagnosed with COVID-19 in two designated hospitals in south China enrolled between Jan 11 and Feb 22, 2020. The urine specimen was collected on admission and applied for pneumococcal urinary antigen tests (PUATs). Demographic, clinical and microbiological data of patients were recorded simultaneously. ResultA total of 146 patients with a confirm diagnosis of COVID-19 at the median age of 50.0 years (IQR 36.0-61.0) were enrolled, in which, 16 (11.0%) were classified as severe cases and 130 (89.0%) as non-severe cases. Of the enrolled patients, only 3 (2.1%) were considered to present the co-infection, in which 1 was co-infected with S.pneumoniae, 1 with B. Ovatus infection and the other one with Influenza A virus infection. Secondary infection occurred in 16 patients, with S. maltophilia as the most commonly isolated pathogen (43.8%), followed by P. aeruginosa (25.0%), E. aerogenes (25.0%), C. parapsilosis (25.0%) and A. fumigates (18.8%). ConclusionPatients with confirmed COVID-19 were rarely co-infected with Streptococcus pneumoniae or other pathogens, indicating that the application of antibiotics against CAP on admission may not be necessary in the treatment of COVID-19 cases.

microbiology↗

bioRxiv2021

Elevated concentration and nitrogen addition affects responses of foliar phosphorus fractions in invasive species to increased phosphorus supply

No studies have explored how the invasive species of Mikania micranatha and Chromolaena odoratan adjust leaf phosphorus (P) among inorganic P (Pi) and organic P fractions to adapt the low soil P availability, especially under elevated CO2 concentrations ([CO2]) and nitrogen (N) deposition. Here, we address this by measuring foliar total N and P concentrations as well as functional P fractions (i.e. Pi, metabolic P, lipid P, nucleic acids P, and residual P) of both invasive species and a native species (Paederia. scandens) growing under different P supplies, N, and N+P addition under both ambient and elevated [CO2]. Phosphorus addition greatly increased plant biomass and foliar P concentrations but did not significantly affect foliar N concentration and leaf mass per unit leaf area (LMA). In response to P addition, the concentration of metabolic P increased the most, followed by that of nucleic acid P, Pi, and lipid P, in all species by an average of 754%, 82%, 53%, and 38%, respectively. However, elevated [CO2] and N addition weakened this positive effect on concentrations of foliar P fractions in the invasive species. Our results indicate that elevated [CO2] and N addition allowed the invasive species to acclimate to a low soil P availability, supporting their successful invasion, through greatly reducing P allocation to non-metabolic foliar P fractions (phospholipids and nucleic acid P) to meet their demand for metabolic P and Pi for photosynthesis, rather than altering LMA.

plant biology↗

bioRxiv2021

Drosophila functional screening of de novo variants in autism uncovers deleterious variants and facilitates discovery of rare neurodevelopmental diseases

Individuals with autism spectrum disorders (ASD) exhibit an increased burden of de novo variants in a broadening range of genes. We functionally tested the effects of ASD missense variants using Drosophila through humanization rescue and overexpression-based strategies. We studied 79 ASD variants in 74 genes identified in the Simons Simplex Collection and found 38% of them caused functional alterations. Moreover, we identified GLRA2 as the cause of a spectrum of neurodevelopmental phenotypes beyond ASD in eight previously undiagnosed subjects. Functional characterization of variants in ASD candidate genes point to conserved neurobiological mechanisms and facilitates gene discovery for rare neurodevelopmental diseases.

genetics↗

bioRxiv2020

Bursting firing in ventromedial hypothalamic neurons exerts dual control of anxiety-like behavior and energy expenditure

Exposure to chronic stress induces anxiety-like behavior and metabolic changes in animals, resulting in adaptive or maladaptive responses to the stressful environment. Recent studies have indicated the dorsomedial ventromedial hypothalamus (dmVMH) as an important hub that regulates both anxiety and energy homeostasis. However, up to now, how dmVMH neurons exert dual control of chronic stress-induced anxiety and energy expenditure remains poorly understood. Here, we established a chronic-stress mouse model that induced anxiety-like behavior, reduced food consumption, and decreased energy expenditure. We found that c-fos expression increased and theta band power is higher in the dmVMH after chronic stress, and the proportion of burst firing neurons significantly increased, which was mediated by elevated expression of T-type calcium channel Cav 3.1. Optogenetically evoked burst firing of dmVMH neurons induced anxiety-like behavior, shifted the respiratory exchange ratio toward fat oxidation, and decreased food intake, while knockdown of Cav3.1 in the dmVMH had the opposite effects. Collectively, our study first revealed an important role of dmVMH burst firing in the dual regulation of anxiety-like behavior and energy expenditure, and identified Cav 3.1 as a crucial regulator of the activity of the burst firing neurons in dmVMH. These molecular and cellular level findings will advance our understanding of the chronic stress-induced emotional malfunction and energy expenditure disorders.

neuroscience↗

bioRxiv2020

Definition of germ cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate

Alternative splicing is critical for development; however, its role in the specification of the three embryonic germ layers is poorly understood. By performing RNA-Seq on human embryonic stem cells (hESCs) and derived definitive endoderm, cardiac mesoderm, and ectoderm cell lineages, we detect distinct alternative splicing programs associated with each lineage. The most prominent splicing program differences are observed between definitive endoderm and cardiac mesoderm. Integrative multi-omics analyses link each program with lineage-enriched RNA binding protein regulators, and further suggest a widespread role for Quaking (QKI) in the specification of cardiac mesoderm. Remarkably, knockout of QKI disrupts the cardiac mesoderm-associated alternative splicing program and formation of myocytes. These changes arise in part through reduced expression of BIN1 splice variants linked to cardiac development. Mechanistically, we find that QKI represses inclusion of exon 7 in BIN1 pre-mRNA via an exonic ACUAA motif, and this is concomitant with intron removal and cleavage from chromatin. Collectively, our results uncover alternative splicing programs associated with the three germ lineages and demonstrate an important role for QKI in the formation of cardiac mesoderm.

molecular biology↗

bioRxiv2020

Central Neural Regulation of Parathyroid Hormone

Parathyroid hormone (PTH) is one of the most important hormones responsible for bone turnover and calcium homeostasis. In mammals, PTH is secreted through the parathyroid glands, unlike in fishes, which are secreted through central nervous system. Studies indicated that a variety of peripheral nerve regulates serum PTH level, however, the mechanism underlying central neural regulation of PTH in mammals remains largely unknown. With an approach including neural-specific retrograde tracing, PTH-Biotin binding assay, and cFos staining, we identified the subfornical organ (SFO) and the paraventricular nucleus (PVN) as two important brain nuclei that responded to serum PTH and calcium changes. Using chemogenetics, we found that serum PTH was suppressed by stimulation of GABAergic neurons in SFO followed by a decrease in trabecular bone mass. Conversely, stimulation of glutamatergic neurons in SFO promoted serum PTH and bone mass. Moreover, we found that the majority of neurons expressing parathyroid hormone 1 receptor (PTH1R) were GABAergic neurons and the majority of neurons expressing parathyroid hormone 2 receptor (PTH2R) were glutamatergic neurons. The paraventricular nucleus (PVN) is downstream of the SFO, and chemogenetic activation of glutamatergic neurons in PVN induced an increase in serum PTH. In summary, our study demonstrates for the first time that distinct neuronal subtypes in the SFO are responsible for bidirectional regulation of serum PTH and bone metabolism, which is mediated through the PVN and the peripheral nervous system. These findings reveal important central neural nodes and will advance our understanding of the central neural regulation of PTH at the molecular, cellular and circuit level.

neuroscience↗

bioRxiv2020

Seeing the forest through the trees: Identifying functional interactions from Hi-C

Eukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensional space. Recent chromosome conformation capture methodologies such as Hi-C have enabled the analysis of interacting regions of the genome providing a valuable insight into the three-dimensional organisation of the chromatin in the nucleus, including chromosome compartmentalisation and gene expression. Complicating the analysis of Hi-C data however is the massive amount of identified interactions, many of which do not directly drive gene function, thus hindering the identification of potentially biologically functional 3D interactions. In this review, we collate and examine the downstream analysis of Hi-C data with particular focus on methods that identify significant functional interactions. We classify three groups of approaches; structurally-associated domain discovery methods e.g. topologically-associated domains and compartments, detection of statistically significant interactions via background models, and the use of epigenomic data integration to identify functional interactions. Careful use of these three approaches is crucial to successfully identifying functional interactions within the genome.

bioinformatics↗

bioRxiv2020

Importin α7 deficiency causes infertility in male mice by disrupting spermatogenesis

Spermatogenesis is driven by an ordered series of events, which rely on trafficking of specific proteins between nucleus and cytoplasm. The importin family of proteins mediates movement of specific cargo proteins when bound to importin {beta}. Importin genes have distinct expression patterns in mouse testis, implying they may have unique roles during mammalian spermatogenesis. Here we use a loss-of-function approach to specifically determine the role of importin 7 in spermatogenesis and male fertility. We show that ablation of importin 7 in male mice leads to infertility and has multiple cumulative effects on both germ cells and Sertoli cells. Importin 7-deficient mice exhibit an impaired Sertoli cell function, including loss of Sertoli cells and a compromised nuclear transport of the androgen receptor. Furthermore, our data demonstrate devastating defects in spermiogenesis that are accompanied by disturbed histone-protamine-exchange, absence of the transcriptional regulator Brwd1 and altered expression of Rfx2 target genes, resulting in incomplete sperm maturation and massive loss of sperms. Our work uncovers the essential role of importin 7 in spermatogenesis and hence in male fertility.

developmental biology↗

bioRxiv2020

Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

Dysfunctional immune response in the COVID-19 patients is a recurrent theme impacting symptoms and mortality, yet the detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 205 COVID-19 patients and controls to create a comprehensive immune landscape. Lymphopenia and active T and B cell responses were found to coexist and associated with age, sex and their interactions with COVID-19. Diverse epithelial and immune cell types were observed to be virus-positive and showed dramatic transcriptomic changes. Elevation of ANXA1 and S100A9 in virus-positive squamous epithelial cells may enable the initiation of neutrophil and macrophage responses via the ANXA1-FPR1 and S100A8/9-TLR4 axes. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis and designing effective therapeutic strategies for COVID-19. HIGHLIGHTSO_LILarge-scale scRNA-seq analysis depicts the immune landscape of COVID-19 C_LIO_LILymphopenia and active T and B cell responses coexist and are shaped by age and sex C_LIO_LISARS-CoV-2 infects diverse epithelial and immune cells, inducing distinct responses C_LIO_LICytokine storms with systemic S100A8/A9 are associated with COVID-19 severity C_LI

genomics↗