Biology subjects

Zhi, H.

Publications and source records attributed to Zhi, H..

12 recordsLinked to original sources

bioRxiv2026

NLR from soybean Rsv1 locus confers broad-spectrum resistance to soybean mosaic virus G1-G7 strains by recognizing viral P3 protein

Nucleotide-binding leucine-rich repeat (NLR) immune receptor genes are of significant value in disease resistance breeding and the control of viral diseases. Soybean mosaic virus (SMV) poses a serious threat to soybean production and the Rsv1 locus in soybean cultivar Suweon 97 confers broad-spectrum resistance against SMV strains G1 to G7; however, this locus harbors no fewer than 18 NLR genes, and thus the broad-spectrum antiviral mechanisms underlying the Rsv1 locus remain poorly understood to date. Here, we established a rapid and highly efficient screening system for cloning NLR genes from soybean Rsv1 locus and identified a broad-spectrum antiviral NLR gene 13g184900 from this highly complicated locus. The NLR encoded by 13g184900 can recognize viral P3 protein from all SMV strains (G1-G7) and another potyvirus Bean common mosaic virus (BCMV). The coiled-coil (CC) domain of this NLR directly interacts with viral P3 protein. Additionally, we showed that this NLR originated from wild soybean accession in East China and has been introduced into several soybean cultivars during domestication. Collectively, we developed a high-throughput screening system for identifying NLR genes in soybean and our study provides new mechanistic perspective on how the Rsv1 locus mediates the broad-spectrum resistance to all SMV G1-G7 strains.

plant biology↗

bioRxiv2025

Metabolic dysfunction related to specific genetic variant sites of methylmalonic acidemia

Methylmalonic acidemia (MMA) is a genetic metabolic disease, with mut (mut-MMA, caused by MMUT gene variation) and cblC (cblC-MMA, caused by MMACHC gene variation) being the predominant subtypes. MMA patients carrying c.729_730insTT and c.609G>A exhibit severe clinical manifestations and have poorer outcomes. Little information is known on the potential mechanism. The metabotypes of MMA patients carrying c.729_730insTT and c.609G>A were profiled. The potential effect of genetic variation sites on the metabolism were explored. Leveraging the gene variation spectrum and the targeted metabolomics, propionic acid, indolelactic acid, myristoleic acid, tetradecenoic acid, tridecanoic acid, and oxoadipic acid showed strong enrichment in c.729_730insTT carrying mut-MMA patients. Whereas mutation c.609G>A caused adipic acid, pimelic acid, fructose, AMP, hexanylcarnitine, and methionine significnatly altered in cblC-MMA patients. Furthermore, the metabolomic profiles were obviously different in c.729_730insTT and non-c.729_730insTT carrying mut-MMA patients after treatment. Different metabolic alterations in cblC-MMA patients carrying c.609G > A and non-c.609G > A under treatment were also observed. Our findings provide unique insights into the metabolic basis of MMA specific subtypes and its implications across different variants.

molecular biology↗

bioRxiv2024

Neurons enhance blood-brain barrier function via upregulating claudin-5 and VE-cadherin expression due to GDNF secretion

Blood-brain barrier (BBB) prevents neurotoxins from entering central nervous system. We aimed to establish and characterize an in vitro triple co-culture BBB model consisting of brain endothelial cells hCMEC/D3, astrocytoma U251 cells, and neuroblastoma SH-SY5Y cells. Co-culture of SH-SY5Y and U251 cells markedly enhanced claudin-5 and VE-cadherin expression in hCMEC/D3 cells, accompanied by increased transendothelial electrical resistance and decreased permeability. Conditioned medium (CM) from SH-SY5Y cells (S-CM), U251 cells (U-CM), and co-culture of SH-SY5Y and U251 cells (US-CM) also promoted claudin-5 and VE-cadherin expression. Glial cell line-derived neurotrophic factor (GDNF) levels in S-CM and US-CM were significantly higher than CMs from hCMEC/D3 and U-CM. Both GDNF and US-CM upregulated claudin-5 and VE-cadherin expression, which were attenuated by anti-GDNF antibody and GDNF signaling inhibitors. GDNF increased claudin-5 expression via the PI3K/AKT/FOXO1 and MAPK/ERK pathways. Meanwhile, GDNF promoted VE-cadherin expression by activating PI3K/AKT/ETS1 and MAPK/ERK/ETS1 signaling. The roles of GDNF in BBB integrity were validated using brain-specific Gdnf silencing mice. The developed triple co-culture BBB model was successfully applied to predict BBB permeability. In conclusion, neurons enhance BBB integrity by upregulating claudin-5 and VE-cadherin expression through GDNF secretion and established triple co-culture BBB model may be used to predict drugs BBB permeability. Impact StatementNeurons and astrocytes enhance the integrity of BBB by releasing GDNF. The released GDNF upregulated claudin-5 and VE-cadherin expression by the activation of PI3K/AKT and MAPK/ERK pathways.

cell biology↗

bioRxiv2023

Leafhopper transmits soybean stay-green associated virus to legume plants

A novel geminivirus, soybean stay-green associated virus (SoSGV), was previously shown to cause soybean delayed senescence and is associated with the incidences of soybean stay-green syndrome. The transmission methods of SoSGV were not yet understood. We captured insects belonging to 24 distinct species in a soybean field with the SoSGV outbreak and detected the presence of SoSGV only in leafhoppers and bean bugs (Riptortus pedestris). Caged feeding experiments using captured leafhoppers and bean bugs from soybean fields showed that leafhoppers, but not bean bugs, are vectors transmitting SoSGV. The common brown leafhopper (Orosius orientalis) is identified as the dominant leafhopper species and can establish colonies feeding on soybean plants in experimental conditions. An investigation of SoSGV defective DNA revealed that soybean genomic DNA could be inserted into the SoSGV genome, while sequences from wild soybean, red bean, and cowpea were also identified. We further showed that the common brown leafhopper could transmit SoSGV to wild soybean and red bean plants, emphasizing the vector role of the leafhopper in the transmission of SoSGV in the field.

microbiology↗

bioRxiv2022

Study on the interactions between cisplatin and cadherin

Cisplatin is an important platinum drug in the chemotherapy of many malignant tumors in clinical application. It is well accepted that its main target is DNA molecule. However, recent studies have shown that platinum drugs may also act on some important functional proteins in the human body and have complicate effects on their efficacy. E-cadherin is newly discovered glycoproteins which have been regarded as the important signs of the occurrence and development of some tumors. In this study, the interactions between cisplatin and E-cadherin were explored by fluorescence spectroscopy and atomic force microscopy (AFM). The fluorescence spectroscopy results indicated that cisplatin can efficiently quench the fluorescence of E-cadherin, and the calculated binding constant Kb was 3.20x106 (25{degrees}C), 1.36 x106(31{degrees}C) and 8.22x105 L mol-1 (37{degrees}C). The thermodynamic parameters {Delta}H <0, {Delta}S <0, {Delta}G <0, reveal that the fluorescence quenching effect of cisplatin on E-cadherin is static quenching, which is dominated by hydrogen bond and van der Waals interaction. The AFM results revealed that there was a staggered interaction between the intermolecular domains of E-cadherin to form a long spherical chain structure. The addition of cisplatin could significantly affect the staggered effect of the E-cadherin molecules. All these results confirmed that there are strong interactions between cisplatin and cadherin.

biochemistry↗

bioRxiv2022

Rsc3K, a SMV resistance gene localized on chromosome 2 in soybean cv. Kefeng No.1, interacts with virulence determinant P3

Soybean mosaic virus (SMV) is one of the most devastating viral pathogens in Glycine max (L.) Merr (soybean). Twenty-two SMV strains (SC1-SC22) isolated in China were identified based on their responses to ten soybean cultivars. By using the F2-derived F3 (F2:3) and recombinant inbred line (RIL) populations of resistant Soybean cultivar (cv.) Kefeng No.1 x susceptible cv. Nannong 1138-2, we localized the gene mediating resistant to SMV-SC3 strain to a 90 kb interval on chromosome 2 in Kefeng No.1. Bean pod mottle virus (BPMV)-induced gene silencing (VIGS) were used to study the gene function of candidate genes in the mapping interval and revealed that an recombinant gene, later named as Rsc3K, caused by internal deletion of a genomic DNA frag ement in Kefeng No.1, is the resistant gene to SMV-SC3. By shuffling genes between avirulent isolate SC3 and avirulent SMV isolate 1129, we found that P3 is the virulence determinant causing resistance on Kefeng No.1. We showed the interaction between Rsc3K and P3 by the yeast two-hybrid (Y2H) and bimolecular fluorescent complementation (BiFC) assays. In conclusion, this study demonstrated that Rsc3K plays a crucial role in resistance of Kefeng No.1 to SMV-SC3 by direct interaction with viral protein P3. HighlightRsc3K resistant to SMV-SC3 by interacting with P3.

molecular biology↗

bioRxiv2021

The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from rubisco. The specialized leaf anatomy required for this separation evolved independently many times. C4 root systems are highly branched, an adaptation thought to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture (RSA). Using a mutant screen in the C4 model plant Setaria italica, we identify siaux1-1 and siaux1-2 as RSA mutants, and use CRISPR/cas9-mediated genome editing and overexpression to confirm the importance of the locus. As AUX1 is not necessary for lateral root emergence in S. viridis, the species from which S. italica was domesticated, we conducted an analysis of auxin responsive elements in the promoters of auxin-responsive gene families in S. italica, and explore the molecular basis of SiAUX1s role in seedling development using an RNAseq analysis of wild type and siaux1-1 plants. Finally, we use a root coordinate system to compare cell-by-cell meristem structures in siaux1-1 and wild type Setaria plants, observing changes in the distribution of cell volumes in all cell layers and a dependence in the frequency of protophloem and protoxylem strands on siAUX1.

plant biology↗

bioRxiv2020

exosome-LncPICALM-AU1 regulates endothelial-mesenchymal transition in hepatopulmonary syndrome

As important mediators of intercellular communication, exosome have can modulate various cellular functions by transferring a variety of intracellular components to target cells. However, little is known about the role of exosome-mediated communication between distant organs. Hepatopulmonary syndrome (HPS) is a severe lung injury caused by chronic liver disease. A new long noncoding RNA (lncRNA) PICALM-AU1 was found and upregulated in the liver of HPS. It was located in the cholangiocytes of liver and then, secreted as exosome into the serum. PICALM-AU1 carrying serum exosomes induced endothelial-mesenchymal transition (EndMT) of PMVECs and promoted lung injury in vivo and in vitro. Furthermore, overexpression of PICALM-AU1 significantly suppressed miR144-3p and subsequently induced ZEB1 expression. Taken together, our findings identified cholangiocyte-derived exosomal lncRNA PICALM-AU1 plays a critical role in the EndMT of HPS lung. And PICALM-AU1 represents a noninvasive biomarker and potential therapeutic target for HPS.

pathology↗

bioRxiv2020

Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut.

Zinc is an essential cofactor for bacterial metabolism, and many Enterobacteriaceae express the zinc transporters ZnuABC and ZupT to acquire this metal in the host. Unexpectedly, the probiotic bacterium Escherichia coli Nissle 1917 exhibited appreciable growth in zinc-limited media even when these transporters were deleted. By utilizing in vitro and in vivo studies, as well as native spray metal infusion mass spectrometry and ion identity molecular networking, we discovered that Nissle utilizes yersiniabactin as a zincophore. Indeed, yersiniabactin enables Nissle to scavenge zinc in zinc-limited media, to resist calprotectin-mediated zinc sequestration, and to thrive in the inflamed gut. Moreover, we discovered that yersiniabactins affinity for iron or zinc changes in a pH-dependent manner, with higher affinity for zinc as the pH increased. Altogether, we demonstrate that siderophore metal affinity can be influenced by the local environment and reveal a mechanism of zinc acquisition available to many commensal and pathogenic Enterobacteriaceae.

microbiology↗

bioRxiv2020

Ion Identity Molecular Networking in the GNPS Environment

Molecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.

bioinformatics↗

bioRxiv2019

Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds

Metals are essential for the molecular machineries of life, and microbes have evolved a variety of small molecules to acquire, compete for, and utilize metals. Systematic methods for the discovery of metal-small molecule complexes from biological samples are limited. Here we describe a two-step native electrospray ionization mass spectrometry method, in which double-barrel post-column metal-infusion and pH adjustment is combined with ion identity molecular networking, a rule-based informatics workflow. This method can be used to identify metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion features with the same chromatographic profiles. As this native metal metabolomics approach can be easily implemented on any liquid chromatography-based mass spectrometry system, this method has the potential to become a key strategy for elucidating and understanding the role of metal-binding molecules in biology.

biochemistry↗

bioRxiv2019

Sex differences in gene expression and proliferation are dependent on the epigenetic modifier HP1γ

Sex differences in growth rate in very early embryos have been recognized in a variety of mammals and attributed to sex-chromosome complement effects as they occur before overt sexual differentiation. We previously found that sex-chromosome complement, rather than sex hormones regulates heterochromatin-mediated silencing of a transgene and autosomal gene expression in mice. Here, sex dimorphism in proliferation was investigated. We confirm that male embryonic fibroblasts proliferate faster than female fibroblasts and show that this proliferation advantage is completely dependent upon heterochromatin protein 1 gamma (HP1{gamma}). To determine whether this sex-regulatory effect of HP1{gamma} was a more general phenomenon, we performed RNA sequencing on MEFs derived from males and females, with or without HP1{gamma}. Strikingly, HP1{gamma} was found to be crucial for regulating nearly all sexually dimorphic autosomal gene expression because deletion of the HP1{gamma} gene in males abolished sex differences in autosomal gene expression. The identification of a key epigenetic modifier as central in defining gene expression differences between males and females has important implications for understanding physiological sex differences and sex bias in disease.

developmental biology↗