Biology subjects

Yuan, G.

Publications and source records attributed to Yuan, G..

At least 37 records · Page 2Linked to original sources

bioRxiv2022

The effector recognition by synthetic sensor NLR receptors requires the concerted action of multiple interfaces within and outside the integrated domain

Plant sensor nucleotide-binding leucine-rich repeat (NLR) receptors detect pathogen effectors through their integrated domains (IDs). The RGA5 sensor NLR recognizes its corresponding effectors AVR-Pia and AVR1-CO39 from the blast fungus Magnaporthe oryzae through direct binding to its heavy metal-associated (HMA) ID to trigger the RGA4 helper NLR-dependent resistance in rice. Here we report a mutant of RGA5 named RGA5HMA5 that confers complete resistance in transgenic rice plants to the M. oryzae strains expressing the noncorresponding effector AVR-PikD. RGA5HMA5 carries three engineered interfaces, two of which lie in the HMA ID and the other in the C-terminal Lys-rich stretch tailing the ID. However, the RGA5 variants having one or two of the three interfaces, including replacing all the Lys residues with Glu residues in the Lys-rich stretch, failed to activate RGA4-dependent cell death of rice protoplasts. Altogether, this work demonstrates that sensor NLRs require a concerted action of multiple surfaces within and outside the IDs to both recognize noncorresponding effectors and activate helper NLR-mediated resistance, and has implications in structure-guided designing of sensor NLRs.

plant biology↗

bioRxiv2022

Homeostatic responses to hypoxia by the carotid body and adrenal medulla are based on mutual antagonism between HIF-1α and HIF-2α

Respiration and blood pressure (BP) are regulated to maintain optimal delivery of O2 to every cell in the body. Arterial hypoxemia is sensed by the carotid body (CB), which initiates sympathetic reflex arcs to the diaphragm to increase ventilation, and to the adrenal medulla (AM) to increase catecholamine secretion and thereby increase BP. However, the underlying molecular mechanisms have not been fully delineated. Here, we report that the relative activities of hypoxia-inducible factor-1 (HIF-1) and HIF-2 determine the set point for the CB and AM, with respect to their maintenance of BP and respiration. In Hif2a+/- mice, which are heterozygous for a knockout allele at the locus encoding HIF-2, expression of HIF-1 and NADPH oxidase 2 was increased in the CB and AM, resulting in an oxidized intracellular redox state with augmented sensitivity to hypoxia, increased BP, and respiratory abnormalities, which were all normalized by treatment with a HIF-1 inhibitor or a superoxide anion scavenger. By contrast, in Hif1a+/- mice, which are heterozygous for a knockout allele at the locus encoding HIF-1, the expression of HIF-2 and superoxide dismutase 2 was increased in the CB and AM, resulting in a reduced intracellular redox state with impaired CB and ventilatory responses to chronic hypoxia, which were normalized by treatment with a HIF-2 inhibitor. None of the abnormalities that were observed in Hif1a+/- or Hif2a+/- mice were observed in Hif1a+/-; Hif2a+/- double- heterozygous mice. Our results demonstrate that redox balance in the CB and AM, which is determined by mutual antagonism between HIF- isoforms, establishes the set point for responses of the CB and AM to hypoxia, and is required for the maintenance of normal BP and respiration.

physiology↗

bioRxiv2021

An intein-mediated split-nCas9 system for base editing in plants

Virus-assisted delivery of the clustered regularly interspaced short palindromic (CRISPR)/CRISPR-associated (Cas) system represents a promising approach for editing plant genomes. However, the relatively large size of the CRISPR/Cas9 system is challenging to package into viral vectors with confined packaging capacity. To address this technical challenge, we developed a strategy that splits the required CRISPR-Cas9 components across a dual-vector system in which CRISPR-Cas reassembles into an active form following co-infection to achieve targeted genome editing in plant cells. An intein-mediated split system was adapted and optimized in plant cells by successfully demonstrating split-eYGFPuv expression. Using a plant-based biosensor, we demonstrated for the first time that the split-SpnCas9 is capable of inducing efficient base editing in plant cells and identified several valid split sites for future biodesign strategies. Overall, this strategy provides new opportunities to bridge different CRISPR/Cas9 tools including base editor, prime editor, and CRISPR activation with virus-mediated gene editing.

plant biology↗

bioRxiv2021

Plant-based biosensors for detecting CRISPR-mediated genome engineering

CRISPR/Cas has recently emerged as the most reliable system for genome engineering in various species. However, concerns about risks associated with CRISPR/Cas9 technology are increasing on potential unintended DNA changes that might accidentally arise from CRISPR gene editing. Developing a system that can detect and report the presence of active CRIPSR/Cas tools in biological systems is therefore very necessary. Here, we developed the real-time detection systems that can spontaneously indicate CRISPR-Cas tools for genome editing and gene regulation including CRISPR/Cas9 nuclease, base editing, prime editing and CRISPRa in plants. Using the fluorescence-based molecular biosensors, we demonstrated that the activities of CRISPR/Cas9 nuclease, base editing, prime editing and CRIPSRa can be effectively detected in transient expression via protoplast transformation and leaf infiltration (in Arabidopsis, poplar, and tobacco) and stable transformation in Arabidopsis.

plant biology↗

bioRxiv2021

Design, synthesis, and characterization of mG2P026 as a high contrast PET imaging ligand for metabotropic glutamate receptor 2

An array of triazolopyridines based on JNJ-46356479 (6) were synthesized as potential PET imaging ligands for metabotropic glutamate receptor 2 (mGluR2) in the brain. The selected candidates 8-11 featured an enhanced positive allosteric modulator (PAM) activity (37-fold max.) and an apparent mGluR2 agonist activity (25-fold max.) compared to compound 6. Radiolabeling of compounds 8 and 9 (also named mG2P026) was achieved via the Cu(I)-mediated radiofluorination in the automated TRACERLabTM FXF-N platform. Both [18F]8 and [18F]9 were obtained with satisfactory radiochemical yields (> 5%, non-decay corrected), high molar activity (> 180 GBq/mol), and excellent chemical and radiochemical purities (> 98%). Preliminary characterization of [18F]8 and [18F]9 in rats confirmed their excellent brain permeability with [18F]9 showing better brain heterogeneity and favorable binding kinetics. Pretreatment with different classes of PAMs enhanced the radioactivity uptake for both [18F]8 and [18F]9 at the regions of interest by 20.3-40.9% and 16.7-81.6%, respectively, due to their pharmacological effects. Further evaluation of [18F]9 in a nonhuman primate confirmed its superior brain heterogeneity in mapping mGlu2 receptors and its higher specific binding than [18F]6. Pretreatment with 0.5 mg/kg BINA led (2) to an enhanced brain uptake of [18F]9 by 3% in high tracer uptake regions that was consistent with the rat studies. Therefore, [18F]9 has the potential to be translated for human studies.

neuroscience↗

bioRxiv2021

PET imaging studies to investigate functional expression of mGluR2 using mG2P001

Metabotropic glutamate receptor 2 (mGluR2) has been extensively studied for the treatment of various neurological and psychiatric disorders. Understanding of the mGluR2 function is pivotal in supporting the drug discovery targeting mGluR2. Herein, the positive allosteric modulation of mGluR2 was investigated via the in vivo positron emission tomography (PET) imaging using 2-((4-(2-[11C]methoxy-4-(trifluoromethyl)phenyl)piperidin-1-yl)methyl)-1-methyl-1H-imidazo[4,5-b]pyridine ([11C]mG2P001).Distinct from the orthosteric compounds, pretreatment with the unlabeled mG2P001, a potent mGluR2 positive allosteric modulator (PAM), resulted in a significant increase instead of decrease of the [11C]mG2P001 accumulation in rat brain detected by PET imaging. Subsequent in vitro studies with [3H]mG2P001 revealed the cooperative binding mechanism of mG2P001 with glutamate and its pharmacological effect that contributed to the enhanced binding of [3H]mG2P001 in transfected CHO cells expressing mGluR2. The in vivo PET imaging and quantitative analysis of [11C]mG2P001 in non-human primates (NHPs) further validated the characteristics of [11C]mG2P001 as an imaging ligand for mGluR2. Self-blocking studies in primates enhanced accumulation of [11C]mG2P001 dose- and delivery-dependently. Altogether, these studies show that [11C]mG2P001 is a sensitive biomarker for mGluR2 expression and the binding is affected by the tissue glutamate concentration.

neuroscience↗

bioRxiv2021

Synthesis and characterization of 5-(2-fluoro-4-pyridine-7-carboxamide as a PET imaging ligand for metabotropic glutamate receptor 2

Metabotropic glutamate receptor 2 (mGluR2) is a therapeutic target for the treatment of several neuropsychiatric disorders and conditions. The role of mGluR2 function in etiology could be unveiled by in vivo imaging using positron emission tomography (PET). In this regard, 5-(2- fluoro-4-[11C]methoxyphenyl)-2,2-dimethyl-3,4-dihydro-2H-pyrano[2,3-b]pyridine-7- carboxamide ([11C]13), a potent negative allosteric modulator (NAM), was developed to support this endeavor. Radioligand [11C]13 was synthesized via the O-[11C]methylation of phenol 24 with a high molar activity of 212 {+/-} 76 GBq/{micro}mol (n = 5) and excellent radiochemical purity (> 99%). PET imaging of [11C]13 in rats demonstrated its superior brain heterogeneity, particularly in the regions of striatum, thalamus, hippocampus, and cortex. Accumulation of [11C]13 in these regions of interest (ROIs) was reduced with pretreatment of mGluR2 NAMs, VU6001966 (9) and MNI-137 (26), the extent of which revealed a time-dependent drug effect of the blocking agents. In a nonhuman primate, [11C]13 selectively accumulated in mGluR2-rich regions, especially in different cortical areas, putamen, thalamus, and hippocampus, and resulted in high-contrast brain images. The regional total volume of distribution (VT) estimates of [11C]13 decreased by 14% after the pretreatment with 9. Therefore, [11C]13 is a potential candidate for translational PET imaging studies of mGluR2 function.

neuroscience↗

bioRxiv2021

Identification of biomarkers and pathways of mitochondria in sepsis patients

Sepsis is a life-threatening condition associate with significant morbidity and mortality, but limited treatment. Mitochondria are recently recognized to be related to the pathophysiology of sepsis, and mitochondria could serve as a potential drug target. In our study, we aim to identify biological functions and pathways of mitochondria during the processes of sepsis by using a bioinformatics method to elucidate their potential pathogenesis. The gene expression profiles of the GSE167914 dataset were originally created by using the Nanostring nCounter Elements TagSet preselected for mitochondrial biogenesis and function panel. The biological pathways were analyzed by the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), Gene Ontology (GO), and Reactome enrichment. KEGG and GO results showed the Neurodegeneration pathways such as Huntington and Parkinson pathways were mostly affected in the development of sepsis. Moreover, we identified several mitochondrial genes including TOMM40, TOMM20, TIMM22, TIMM10, TIMM17A, TIMM9, TIMM44 were involved in the regulation of protein translocation into mitochondria. Further, we predicted several regulators that had the ability to affect the mitochondria during sepsis by L1000fwd analysis. Thus, this study provides further insights into the mechanism of mitochondrial function during sepsis.

immunology↗

bioRxiv2021

Identification of biomarkers and candidate regulators for multiple myeloma under the knockout of AURKA

Multiple myeloma (MM) is a plasma cell malignancy that is characterized by the overabundance of monoclonal paraprotein. Aurora kinase A (AURKA) was upregulated in patients with high-risk MM. AURKA inhibitors were used to inhibit MM cell proliferation by inducing cell apoptosis and injury. In our study, we aim to identify biological processes and pathways of MM cells under the knockout of AURKA (AURKA KO) by using a bioinformatics method to elucidate their potential pathogenesis. The gene expression profiles of the GSE163589 dataset were originally produced by using the high-throughput BGISEQ-500 (Homo sapiens). The biological categories and pathways were analyzed by the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), Gene Ontology (GO), and Reactom enrichment. KEGG and GO results indicated the biological pathways related to the immune responses and cancer activities were mostly affected in the development of MM with AURKA KO. Moreover, we identified several genes including GNG5, UBE2D1, and BUB1B were involved in the regulation of cancer genesis. We further predicted novel regulators that had the ability to affect the progression of MM with AURKA KO based on the L1000fwd analysis. Therefore, this study provides further insights into the mechanism of MM under AURKA inhibitor treatments.

immunology↗

bioRxiv2021

Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that [~]30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction. HighlightOur manuscript presents a high-quality reference genome of the inbred line A188, and provides new insights into candidate genes underlying maize embryonic callus induction and other maize agronomic traits.

genetics↗

bioRxiv2021

Identification of biomarkers and candidate inhibitors for multiple myeloma

Multiple myeloma (MM) is a plasma cell malignancy that causes the overabundance of monoclonal paraprotein (M protein) and organ damages. In our study, we aim to identify biological markers and processes of MM using a bioinformatics method to elucidate their potential pathogenesis. The gene expression profiles of the GSE153626 datasets were originally produced by using the high-throughput Illumina HiSeq 4000 (Mus musculus). The functional categories and biochemical pathways were identified and analyzed by the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), Gene Ontology (GO), and Reactom enrichment. KEGG and GO results showed the biological pathways related to immune dysfunction and signal transduction are mostly affected in the development of MM. Moreover, we identified several genes including Gngt2, Foxp3, and Cd3g were involved in the regulation of immune cells. We further predicted new inhibitors that have the ability to block the progression of MM based on the L1000fwd analysis. Therefore, this study provides further insights into the underlying pathogenesis of MM.

bioinformatics↗

bioRxiv2020

Identification of specific biomarkers and pathways in the synovial tissues of patients with osteoarthritis in comparison to rheumatoid arthritis

Osteoarthritis and rheumatoid arthritis are two common arthritis with different pathogenesis. Here, we explore the difference of genes and biological pathways in human synovial fibroblasts by using a bioinformatics method to clarify their potential pathogenesis. The GSE7669 dataset was originally produced by using an Affymetrix Human Genome U95 platform. We used the KEGG and GO analysis to identify the functional categories and pathways. Our results suggested that biological adhesion and cell adhesion are the main signaling pathways in osteoarthritis in comparison to rheumatoid arthritis. Furthermore, Albumin, MAPK3, PTPRC, COL1A1, and CXCL12 may be key genes in osteoarthritis. Therefore, our study provides potential targets for the specific and accurate therapy of osteoarthritis.

molecular biology↗

bioRxiv2020

Identification of potential key genes for SARS-CoV-2 infected human bronchial organoids based on bioinformatics analysis

There is an urgent need to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) that leads to COVID-19 and respiratory failure. Our study is to discover differentially expressed genes (DEGs) and biological signaling pathways by using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profiles of the GSE150819 datasets were originally produced using an Illumina NextSeq 500 (Homo sapiens). KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) were utilized to identify functional categories and significant pathways. KEGG and GO results suggested that the Cytokine-cytokine receptor interaction, P53 signaling pathway, and Apoptosis are the main signaling pathways in SARS-CoV-2 infected human bronchial organoids (hBOs). Furthermore, NFKBIA, C3, and CCL20 may be key genes in SARS-CoV-2 infected hBOs. Therefore, our study provides further insights into the therapy of COVID-19.

bioinformatics↗

bioRxiv2020

Identification of key genes in SARS-CoV-2 patients on bioinformatics analysis

The COVID-19 pandemic has infected millions of people and overwhelmed many health systems globally. Our study is to identify differentially expressed genes (DEGs) and associated biological processes of COVID-19 using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profiles of the GSE152075 datasets were originally produced by using the high-throughput Illumina NextSeq 500. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed to identify functional categories and biochemical pathways. GO and KEGG results suggested that several biological pathways such as "Fatty acid metabolism" and "Cilium morphogenesis" are mostly involved in the development of COVID-19. Moreover, several genes are critical for virus invasion and adhesion including FLOC, DYNLL1, FBXL3, and FBXW11 and show significant differences in COVID-19 patients. Thus, our study provides further insights into the underlying pathogenesis of COVID-19.

bioinformatics↗

bioRxiv2020

Comparative secretome of Magnaporthe oryzae identified proteins involved in virulence and cell wall integrity

Plant fungal pathogens secrete numerous proteins into the apoplast at the plant-fungus contact sites to facilitate colonization. Only a few secreted proteins were functionally characterized in Magnaporthe oryzae, the fungal pathogen causing rice blast disease worldwide. ALG3 is an -1, 3-mannosyltransferase function in N-glycan synthesis for secreted N-glycosylated proteins, and the {Delta}alg3 mutants show strong defects in cell wall integrity and fungal virulence, indicating a potential effect on the secretion of multiple proteins. In this study, we compared the secretome of wild type and {Delta}alg3 mutants, and identified 51 proteins that require ALG3 for proper secretion. These are predicted to be involved in metabolic processes, interspecies interactions, cell wall organization, and response to chemicals. The tested secreted proteins localized at the apoplast region surrounding the fungal infection hyphae. Moreover, the N-glycosylation of candidate proteins was significantly changed in the {Delta}alg3 mutant, leading to the reduction of protein secretion and abnormal protein localization. Furthermore, we tested the function of two genes, one is a previously reported M. oryzae gene Invertase 1 (INV1) encoding a secreted invertase, and the other one is a gene encoding an Acid mammalian chinitase (AMCase). The fungal virulence was significantly reduced and the cell wall integrity was altered in the {Delta}inv1 and {Delta}amcase mutant strains. Elucidation of the comparative secretome of M. oryzae improves our understanding of the proteins that require ALG3 for secretion, and of their function in fungal virulence and cell wall integrity.

plant biology↗

bioRxiv2019

Enhancer-dependence of gene expression increases with developmental age

How overall principles of gene regulation (the \"logic\") may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic and topological profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1 and Myb occupancy. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes employ distal enhancers for long-range regulation through enhancer-promoter looping, confirmed by Gata1 HiChIP. Genome editing demonstrated distal enhancers are required for gene expression in EryD but not in EryP. Applying a metric for enhancer-dependence of transcription, we observed a progressive reliance on enhancer control with increasing age of ontogeny among diverse primary cells and tissues of mouse and human origin. Our findings highlight fundamental and conserved differences in regulatory logic at distinct developmental stages, characterized by simpler promoter-centric regulation in embryonic cells and combinatorial enhancer-driven control in adult cells.\n\nHighlightsO_LIRegulation of embryonic-specific erythroid genes is promoter-centric through Gata1\nC_LIO_LIAdult-specific control is combinatorial enhancer-driven and requires Myb\nC_LIO_LIAdult specific genes have increased enhancer-promoter chromatin interactions\nC_LIO_LIEnhancer-dependence increases progressively with increasing developmental age\nC_LI

molecular biology↗

bioRxiv2019

Kaposi sarcoma-associated herpesvirus infection in HIV patients: potential role of HIV-associated extracellular vesicles

Kaposi sarcoma-associated herpesvirus (KSHV) is the causal agent for Kaposi sarcoma (KS), the most common malignancy in people living with HIV/AIDS. The oral cavity is a major route for KSHV infection and transmission. However, how KSHV breaches the oral epithelial barrier for spreading to the body is not clear. Here we show that extracellular vesicles (EVs) purified from saliva of HIV-positive individuals and secreted by HIV-1-infected T cells promote KSHV infectivity in both monolayer and 3-dimensional models of immortalized and primary human oral epithelial cells, establishing the latency of the virus. The HIV trans-activation response (TAR) element RNA in HIV-associated EVs contributes to the infectivity of KSHV through the epidermal growth factor receptor (EGFR). Cetuximab, a monoclonal neutralizing antibody to EGFR, blocks HIV-associated EV-enhanced KSHV infection. Our findings reveal that saliva containing HIV-associated EVs is a risk factor for enhancement of KSHV infection and that inhibition of EGFR serves as a novel strategy for controlling KSHV infection and transmission in the oral cavity.\n\nAuthor summaryKaposi sarcoma-associated herpesvirus (KSHV) is a causal agent for Kaposi sarcoma (KS), the most common malignancy in HIV/AIDS patients. Oral transmission through saliva is considered the most common route for spreading of the virus among HIV/AIDS patients. However, the role of HIV-specific components in co-transfection of KSHV is unclear. We demonstrate that extracellular vesicles (EV) purified from saliva of HIV patients and secreted by HIV-infected T cells promote KSHV infectivity in immortalized and primary oral epithelial cells. HIV-associated EVs promote KSHV infection depends on the HIV trans-activation element (TAR) RNA and EGFR of oral epithelial cells, both can be targeted for reducing KSHV infection. These results reveal that HIV-EVs is a risk factor for KSHV co-infection in the HIV-infected population.

microbiology↗

bioRxiv2018

Biolistic transformation of Haematococcus pluvialis with constructs based on the flanking sequences of its endogenous alpha tubulin gene

The complete sequence information of the alpha tubulin (tub) genes was obtained from both Haematococcus pluvialis NIES144 and SCCAP K0084., Putative transcriptional elements and polyadenylation signals were identified respectively in their 5 and 3 flanking regions. Three selection cassettes of tub/aadA, tub/hyr and tub/ble with 3 different antibiotic-resistant genes fused between the 5 and 3 flanking sequences of the tub gene were constructed and utilized for biolistic transformation of H.pluvialis. Antibiotic resistant transformants were obtained in the bombardments with the tub/aadA cassette in 2 strains. It was found that, the foreign tub/aadA DNA could be completely transferred and inherited in their genome through non-homologous recombination. Moreover, transcripts of the insert and spectinomycin resistance were identified. Transformation efficiencies up to 3x10-5 per g DNA could be obtained in H.pluvialis NIES144 or SCCAP K0084 through utilization of a culture with a high percentage of flagellate cells and by optimizing bombarding protocol. The presented selection marker and optimized transforming procedures in this report should strengthen the platform technology for genetical manipulation and modification of H.pluvialis.

molecular biology↗