7 results on '"Runyu Yao"'
Search Results
2. Antibacterial Activity and Transcriptomic Analysis of Hesperetin against Alicyclobacillus acidoterrestris Vegetative Cells
- Author
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Siqi Zhao, Yanzi Nan, Runyu Yao, Langhong Wang, Xinan Zeng, Rana Muhammad Aadil, and Muhammad Asim Shabbir
- Subjects
Alicyclobacillus acidoterrestris ,hesperetin ,antibacterial activity ,antibacterial mechanism ,transcriptomic analysis ,Chemical technology ,TP1-1185 - Abstract
The aim of this research was to investigate the antimicrobial characteristics and mechanism of hesperetin against Alicyclobacillus acidoterrestris vegetative cells. The results presented show that hesperetin had effective antimicrobial activity on Alicyclobacillus acidoterrestris vegetative cells, minimum inhibition concentration (MIC) of 0.0625 g/L, and minimum bacterial concentration (MBC) greater than 2 g/L. Moreover, treatment of hesperetin caused significant damage to cell integrity, preventing the growth of Alicyclobacillus acidoterrestris vegetative cells, enhancing the leakage of nucleic acid and proteins, and destroying the vegetative cell morphology. To further investigate the mechanism, transcriptomic analysis was carried out, and 3056 differentially expressed genes (DEGs) were detected. Gene ontology (GO) enrichment analysis revealed that hesperetin inhibits Alicyclobacillus acidoterrestris by affecting the intracellular nitrogen metabolism and amino acid metabolism. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis explained that hesperetin was also able to prevent the growth of Alicyclobacillus acidoterrestris by affecting the processes of nutrient transport, energy metabolism, and flagella motility. These results provide new insights into the antimicrobial effects and mechanism of hesperetin against Alicyclobacillus acidoterrestris, which provides a new method for inactive Alicyclobacillus acidoterrestris in the juice industry.
- Published
- 2023
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- View/download PDF
3. Phenotype-based drug screening: An in vivo strategy to classify and identify the chemical compounds modulating zebrafish M-cell regeneration
- Author
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Ankita Kumari, Xin-An Zeng, Abdul Rahaman, Muhammad Adil Farooq, Yanyan Huang, Mahafooj Alee, Runyu Yao, Murtaza Ali, Ibrahim Khalifa, and Omnia Badr
- Subjects
phenotype drug screening (PDS) ,regeneration ,zebrafish ,axon ,M-cell ,Biology (General) ,QH301-705.5 - Abstract
Several disease-modulatory FDA-approved drugs are being used in patients with neurodegenerative diseases. However, information on their toxicity-related profiles is very limited. Therefore, measurement of drug toxicity is essential to increase the knowledge of their side effects. This study aimed to identify compounds that can modulate M-cell regeneration by causing neuro-protection and -toxicity. Here, we developed a simple and efficient in vivo assay using Tg (hsp: Gal4FF62A; UAS: nfsB-mCherry) transgenic zebrafish larvae. Interestingly, via the phenotype-based drug screening approach, we rapidly investigated 1,260 compounds from the United States drug collection and validated these in large numbers, including 14 compounds, that were obstructing this regeneration process. Next, 4 FDA-approved drugs out of 14 compounds were selected as the lead hits for in silico analysis to clarify their binding patterns with PTEN and SOCS3 signaling due to their significant potential in the inhibition of axon regeneration. Molecular docking studies indicated good binding affinity of all 4 drugs with the respective signaling molecules. This may point to PTEN and SOCS3 as the signaling molecules responsible for reducing axon regeneration. Moreover, the acute effect of compounds in reducing M-cell regeneration delineated their toxic effect. In conclusion, our in vivo along with in silico screening strategy will promote the rapid translation of new therapeutics to improve knowledge of the toxicity profile of approved/non-approved drugs efficiently.
- Published
- 2022
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4. Temporal Cortex Microarray Analysis Revealed Impaired Ribosomal Biogenesis and Hyperactivity of the Glutamatergic System: An Early Signature of Asymptomatic Alzheimer's Disease
- Author
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Ankita Kumari, Abdul Rahaman, Xin-An Zeng, Muhammad Adil Farooq, Yanyan Huang, Runyu Yao, Murtaza Ali, Romana Ishrat, and Rafat Ali
- Subjects
microarray ,Alzheimer ,symptomatic ,asymptomatic ,genes ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Pathogenic aging is regarded as asymptomatic AD when there is no cognitive deficit except for neuropathology consistent with Alzheimer's disease. These individuals are highly susceptible to developing AD. Braak and Braak's theory specific to tau pathology illustrates that the brain's temporal cortex region is an initiation site for early AD progression. So, the hub gene analysis of this region may reveal early altered biological cascades that may be helpful to alleviate AD in an early stage. Meanwhile, cognitive processing also drags its attention because cognitive impairment is the ultimate result of AD. Therefore, this study aimed to explore changes in gene expression of aged control, asymptomatic AD (AsymAD), and symptomatic AD (symAD) in the temporal cortex region. We used microarray data sets to identify differentially expressed genes (DEGs) with the help of the R programming interface. Further, we constructed the protein-protein interaction (PPI) network by performing the STRING plugin in Cytoscape and determined the hub genes via the CytoHubba plugin. Furthermore, we conducted Gene Ontology (GO) enrichment analysis via Bioconductor's cluster profile package. Resultant, the AsymAD transcriptome revealed the early-stage changes of glutamatergic hyperexcitability. Whereas the connectivity of major hub genes in this network indicates a shift from initially reduced rRNA biosynthesis in the AsymAD group to impaired protein synthesis in the symAD group. Both share the phenomenon of breaking tight junctions and others. In conclusion, this study offers new understandings of the early biological vicissitudes that occur in the brain before the manifestation of symAD and gives new promising therapeutic targets for early AD intervention.
- Published
- 2022
- Full Text
- View/download PDF
5. Temporal Cortex Microarray Analysis Revealed Impaired Ribosomal Biogenesis and Hyperactivity of the Glutamatergic System: An Early Signature of Asymptomatic Alzheimer's Disease.
- Author
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Kumari, Ankita, Rahaman, Abdul, Xin-An Zeng, Farooq, Muhammad Adil, Yanyan Huang, Runyu Yao, Ali, Murtaza, Ishrat, Romana, and Ali, Rafat
- Subjects
ALZHEIMER'S disease ,TEMPORAL lobe ,GENE regulatory networks ,HYPERACTIVITY ,PROTEIN synthesis - Abstract
Pathogenic aging is regarded as asymptomatic AD when there is no cognitive deficit except for neuropathology consistent with Alzheimer's disease. These individuals are highly susceptible to developing AD. Braak and Braak's theory specific to tau pathology illustrates that the brain's temporal cortex region is an initiation site for early AD progression. So, the hub gene analysis of this region may reveal early altered biological cascades that may be helpful to alleviate AD in an early stage. Meanwhile, cognitive processing also drags its attention because cognitive impairment is the ultimate result of AD. Therefore, this study aimed to explore changes in gene expression of aged control, asymptomatic AD (AsymAD), and symptomatic AD (symAD) in the temporal cortex region. We used microarray data sets to identify differentially expressed genes (DEGs) with the help of the R programming interface. Further, we constructed the protein-protein interaction (PPI) network by performing the STRING plugin in Cytoscape and determined the hub genes via the CytoHubba plugin. Furthermore, we conducted Gene Ontology (GO) enrichment analysis via Bioconductor's cluster profile package. Resultant, the AsymAD transcriptome revealed the early-stage changes of glutamatergic hyperexcitability. Whereas the connectivity of major hub genes in this network indicates a shift from initially reduced rRNA biosynthesis in the AsymAD group to impaired protein synthesis in the symAD group. Both share the phenomenon of breaking tight junctions and others. In conclusion, this study offers new understandings of the early biological vicissitudes that occur in the brain before the manifestation of symAD and gives new promising therapeutic targets for early AD intervention. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
6. A glucuronokinase gene in Arabidopsis, AtGlcAK, is involved in drought tolerance by modulating sugar metabolism
- Author
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Ji Huang, Jinyan Li, Xiaoxun Zhou, Congying Yuan, Hongping Chang, Shuai Hu, Wenjun Xiao, Meiling Li, Cheng Zhang, Shucan Liu, Runyu Yao, Xinhong Guo, and Jingru Luo
- Subjects
0106 biological sciences ,0301 basic medicine ,Osmotic shock ,biology ,fungi ,Drought tolerance ,Mutant ,food and beverages ,Plant Science ,Carbohydrate metabolism ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Biochemistry ,Glucuronokinase ,Arabidopsis ,Molecular Biology ,Abscisic acid ,Lateral root formation ,010606 plant biology & botany - Abstract
Arabidopsis glucuronokinase (AtGlcAK), as a member of the GHMP kinases family, is implicated in the de novo synthesis of UDP-glucuronic acid (UDP-GlcA) by the myo-inositol oxygenation pathway. In this study, two T-DNA insertion homozygous mutants of AtGlcAK, atglcak-1 and atglcak-2, were identified. AtGlcAK was highly expressed in roots and flowers. There was reduced primary root elongation and lateral root formation in atglcak mutants under osmotic stress. The atglcak mutants displayed enhanced stomatal opening in response to abscisic acid (ABA), elevated water loss and impaired drought tolerance. Under water stress, the accumulation of reducing and soluble sugars was reduced in atglcak mutants, and the metabolism of glucose and sucrose was affected by the synthetic pathway of UDP-GlcA. Furthermore, a reduced level of starch in atglcak mutants was observed under normal conditions. The phylogenetic analysis suggested that GlcAK was conserved in numerous dicots and monocots plants. In short, AtGlcAK mutants displayed hypersensitivity to ABA and reduced root development under water stress, rendering the plants more susceptible to drought stress.
- Published
- 2017
- Full Text
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7. Genome-wide identification, classification and expression analysis of GHMP genes family in Arabidopsis thaliana
- Author
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Ping Zhou, Rong Hu, Hongping Chang, Runyu Yao, Xiutao Lu, Cheng Zhang, Wenjun Xiao, Lijun Cai, Xinhong Guo, Congying Yuan, and Zhuang He
- Subjects
Genetics ,Abiotic stress ,Phosphomevalonate kinase ,Homoserine ,Plant Science ,Biology ,biology.organism_classification ,Genome ,chemistry.chemical_compound ,chemistry ,Multiple EM for Motif Elicitation ,Arabidopsis thaliana ,Gene ,Ecology, Evolution, Behavior and Systematics ,Function (biology) - Abstract
The GHMP genes family, a unique class of ATP-dependent enzymes, consists of galactokinases, homoserine kinases, mevalonate kinases and phosphomevalonate kinase etc. It was implicated in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. Previous studies mainly focused on the structure, catalytic mechanism or function in abiotic stress signaling. In this study, we integrated the research progress on GHMP genes and identified 12 members (five previously discovered and seven newly identified here) of this family in Arabidopsis thaliana. The gene ontology, phylogenetic relationship, motifs, cis-acting element, expression profiles, structures and protein–protein interaction network of GHMP family were analyzed. The neighbor-joining tree and cluster of gene structures indicated that the 12 members were divided into two classes. The three motifs in the GHMP family were highly conserved among the GHMP family by Multiple EM for Motif Elicitation, providing further proof on their phylogenetic relationship. Additionally, prediction on cis-acting elements indicated that these genes were likely to be involved in multiple responses stimulated by various hormones and abiotic stress. It is roughly consistent with the data of microarray. The identification and bioinformatic analysis of GHMP family in Arabidopsis thaliana could provide reference data for further study on their biological functions, especially in the responsiveness to hormones and stress signaling.
- Published
- 2015
- Full Text
- View/download PDF
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