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Yang Y, Wang H, Tu J, Li Y, Guan H. Comprehensive genomic analysis of Burkholderia arboris PN-1 reveals its biocontrol potential against Fusarium solani-induced root rot in Panax notoginseng. Curr Genet 2024; 70:4. [PMID: 38555312 DOI: 10.1007/s00294-024-01288-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Panax notoginseng (Burkill) F.H. Chen, a valuable traditional Chinese medicine, faces significant yield and quality challenges stemming from root rot primarily caused by Fusarium solani. Burkholderia arboris PN-1, isolated from the rhizosphere soil of P. notoginseng, demonstrated a remarkable ability to inhibit the growth of F. solani. This study integrates phenotypic, phylogenetic, and genomic analyses to enhance our understanding of the biocontrol mechanisms employed by B. arboris PN-1. Phenotype analysis reveals that B. arboris PN-1 effectively suppresses P. notoginseng root rot both in vitro and in vivo. The genome of B. arboris PN-1 comprises three circular chromosomes (contig 1: 3,651,544 bp, contig 2: 1,355,460 bp, and contig 3: 3,471,056 bp), with a 66.81% GC content, housing 7,550 protein-coding genes. Notably, no plasmids were detected. Phylogenetic analysis places PN-1 in close relation to B. arboris AU14372, B. arboris LMG24066, and B. arboris MEC_B345. Average nucleotide identity (ANI) values confirm the PN-1 classification as B. arboris. Comparative analysis with seven other B. arboris strains identified 4,628 core genes in B. arboris PN-1. The pan-genome of B. arboris appears open but may approach closure. Whole-genome sequencing revealed 265 carbohydrate-active enzymes and identified 9 gene clusters encoding secondary metabolites. This comprehensive investigation enhances our understanding of B. arboris genomes, paving the way for their potential as effective biocontrol agents against fungal plant pathogens in the future.
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Affiliation(s)
- Yun Yang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan, China
| | - Haoji Wang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Jielei Tu
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Yan Li
- Yunnan Provincial Rural Energy Management Station, Kunming, 650233, Yunnan, China
| | - Huilin Guan
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China.
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China.
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Xuan X, Ruan J, Wu C, Gao Y, Li L, Lei X. A TTC19 mutation associated with progressive movement disorders and peripheral neuropathy: Case report and systematic review. CNS Neurosci Ther 2024; 30:e14425. [PMID: 37927170 PMCID: PMC10948947 DOI: 10.1111/cns.14425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/30/2023] [Accepted: 08/14/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Mitochondrial complex III (CIII) deficiency is an autosomal recessive disease characterized by symptoms such as ataxia, cognitive dysfunction, and spastic paraplegia. Multiple genes are associated with complex III defects. Among them, the mutation of TTC19 is a rare subtype. METHODS We screened a Chinese boy with weakness of limbs and his non-consanguineous parents by whole exome sequencing and targeted sequencing. RESULTS We report a Chinese boy diagnosed with mitochondrial complex III defect type 2 carrying a homozygous variant (c.719-732del, p.Leu240Serfs*17) of the TTC19 gene. According to the genotype analysis of his family members, this is an autosomal recessive inheritance. We provide his clinical manifestation. CONCLUSIONS A new type of TTC19 mutation (c.719-732del, p.Leu240Serfs*17) was found, which enriched the TTC19 gene mutation spectrum and provided new data for elucidating the pathogenesis of CIII-deficient diseases.
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Affiliation(s)
- Xianjun Xuan
- Department of NeurologyHangzhou Ninth People's HospitalHangzhouChina
| | - Jie Ruan
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, Department of Clinical Pharmacy, the First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Chunhong Wu
- Department of NeurologyHangzhou Ninth People's HospitalHangzhouChina
| | - Yiyi Gao
- Ningbo Medical Center Lihuili HospitalNingboChina
| | - Lingfei Li
- Department of Neurology, Affiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouChina
| | - Xiaoguang Lei
- First Department of Neurology, First Affiliated Hospital of Kunming Medical UniversityKunming Medical UniversityKunmingChina
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Zhang LM, Liang XL, Xiong GF, Xing XL, Zhang QJ, Zhang BR, Liu MW. Analysis and identification of oxidative stress-ferroptosis related biomarkers in ischemic stroke. Sci Rep 2024; 14:3803. [PMID: 38360841 PMCID: PMC10869843 DOI: 10.1038/s41598-024-54555-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/14/2024] [Indexed: 02/17/2024] Open
Abstract
Studies have shown that a series of molecular events caused by oxidative stress is associated with ferroptosis and oxidation after ischemic stroke (IS). Differential analysis was performed to identify differentially expressed mRNA (DEmRNAs) between IS and control groups. Critical module genes were identified using weighted gene co-expression network analysis (WGCNA). DEmRNAs, critical module genes, oxidative stress-related genes (ORGs), and ferroptosis-related genes (FRGs) were crossed to screen for intersection mRNAs. Candidate mRNAs were screened based on the protein-protein interaction (PPI) network and the MCODE plug-in. Biomarkers were identified based on two types of machine learning algorithms, and the intersection was obtained. Functional items and related pathways of the biomarkers were identified using gene set enrichment analysis (GSEA). Finally, single-sample GSEA (ssGSEA) and Wilcoxon tests were used to identify differential immune cells. An miRNA-mRNA-TF network was created. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the expression levels of biomarkers in the IS and control groups. There were 8287 DE mRNAs between the IS and control groups. The genes in the turquoise module were selected as critical module genes for IS. Thirty intersecting mRNAs were screened for overlaps. Seventeen candidate mRNAs were also identified. Four biomarkers (CDKN1A, GPX4, PRDX1, and PRDX6) were identified using two types of machine-learning algorithms. GSEA results indicated that the biomarkers were associated with steroid biosynthesis. Nine types of immune cells (activated B cells and neutrophils) were markedly different between the IS and control groups. We identified 3747 miRNA-mRNA-TF regulatory pairs in the miRNA-mRNA-TF regulatory network, including hsa-miR-4469-CDKN1A-BACH2 and hsa-miR-188-3p-GPX4-ATF2. CDKN1A, PRDX1, and PRDX6 were upregulated in IS samples compared with control samples. This study suggests that four biomarkers (CDKN1A, GPX4, PRDX1, and PRDX6) are significantly associated with IS. This study provides a new reference for the diagnosis and treatment of IS.
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Affiliation(s)
- Lin-Ming Zhang
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Xing-Ling Liang
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Gui-Fei Xiong
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Xuan-Lin Xing
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Qiu-Juan Zhang
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Bing-Ran Zhang
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Ming-Wei Liu
- Department of Emergency, People's Hospital of Dali Bai Autonomous Prefecture, No. 35 Renmin South Road, Xiaguan Street, Dalí, 671000, Yunnan, China.
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Xie ZY, Cao G, Chen JJ, Chen TT, Sun LJ, Li YX, Zu WL, Ye JJ, Du YX, Zhao ZG, Ye HF. [Investigation and analysis on the detection of IgG antibodies against the rubella virus among rural childbearing-age women in preconception period in Yunnan Province from 2013 to 2019]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:2134-2139. [PMID: 38186167 DOI: 10.3760/cma.j.cn112150-20230118-00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A study was conducted on rural women of childbearing age aged 20-49 who underwent the National Free Preconception Health Examination Project (NFPHEP)in Yunnan Province from 2013 to 2019. Descriptive analysis was conducted to determine the negative rate of IgG antibodies against the rubella virus and its differences among various socio-demographic characteristics. Among the 1 511 203 study subjects, the negative rate of IgG antibodies against the rubella virus was 24.36%. Only 2.64% of the population had received rubella virus vaccine. The negative rate of IgG antibodies among rural childbearing-age women in the preconception period in Yunnan Province decreased with age and educational level (Ptrend<0.001). The negative rate of IgG antibodies in ethnic minority women of childbearing age in the preconception period (25.19%) was higher than that of Han women (23.88%). Among the 22 ethnic groups with over 1 000 participants, the negative rates of IgG antibodies in women of childbearing age from the Blang (32.85%), Bouyei (31.03%), Zhuang (31.01%), and Miao (30.70%) ethnic groups were higher than those of women from other ethnic groups. Among the 16 states (cities) in Yunnan Province, the negative rate of IgG antibodies in pregnant women of childbearing age in Wenshan Zhuang and Miao Autonomous Prefecture (38.06%) and Lincang City (32.63%) was higher than that in other states (cities). The negative rate of serum IgG antibodies in women who reported having received rubella virus vaccine (18.60%) was lower than that in other non-vaccinated populations (24.52%). The proportion of rural women of childbearing age in Yunnan Province who were susceptible to the rubella virus before pregnancy was still high. It is necessary to promote rubella vaccination among people susceptible to rubella, especially pregnant women, to prevent rubella virus infection and reduce the incidence rate and disease burden of rubella people.
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Affiliation(s)
- Z Y Xie
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - G Cao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education,Yunnan University/Yunnan Provincial Center for Research & Development of Natural Products/School of Pharmacy,Yunnan University, Kunming 650500, China
| | - J J Chen
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - T T Chen
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - L J Sun
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - Y X Li
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - W L Zu
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - J J Ye
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - Y X Du
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - Z G Zhao
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
| | - H F Ye
- Population and Family Planning Institute of Yunnan Province/NHC Key Laboratory of Periconception Health Birth in Western China,Kunming 650021,China
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Chen J, Liu Y, Yang M, Shi X, Mei Y, Li J, Yang C, Pu S, Wen J. Analysis of the Differences in Volatile Organic Compounds in Different Rice Varieties Based on GC-IMS Technology Combined with Multivariate Statistical Modelling. Molecules 2023; 28:7566. [PMID: 38005287 PMCID: PMC10673298 DOI: 10.3390/molecules28227566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
In order to investigate the flavour characteristics of aromatic, glutinous, and nonaromatic rice, gas chromatography-ion mobility spectrometry (GC-IMS) was used to analyse the differences in volatile organic compounds (VOCs) amongst different rice varieties. The results showed that 103 signal peaks were detected in these rice varieties, and 91 volatile flavour substances were identified. Amongst them, 28 aldehydes (28.89~31.17%), 24 alcohols (34.85~40.52%), 14 ketones (12.26~14.74%), 12 esters (2.30~4.15%), 5 acids (7.80~10.85%), 3 furans (0.30~0.68%), 3 terpenes (0.34~0.64%), and 2 species of ethers (0.80~1.78%) were detected. SIMCA14.1 was used to perform principal component analysis (PCA) and orthogonal partial least squares discriminant analysis, and some potential character markers (VIP > 1) were further screened out of the 91 flavour substances identified based on the variable important projections, including ethanol, 1-hexanol, hexanal, heptanal, nonanal, (E)-2-heptenal, octanal, trans-2-octenal, pentanal, acetone, 6-methyl-5-hepten-2-one, ethyl acetate, propyl acetate, acetic acid, and dimethyl sulphide. Based on the established fingerprint information, combined with principal component analysis and orthogonal partial least squares discriminant analysis, different rice varieties were also effectively classified, and the results of this study provide data references for the improvement in aromatic rice varieties.
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Affiliation(s)
- Jin Chen
- Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China; (J.C.); (Y.L.)
| | - Ying Liu
- Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China; (J.C.); (Y.L.)
| | - Mi Yang
- Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China; (J.C.); (Y.L.)
| | - Xinmin Shi
- Lincang Seed Management Station, Lincang 677000, China
| | - Yuqin Mei
- Lincang Seed Management Station, Lincang 677000, China
| | - Juan Li
- Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China; (J.C.); (Y.L.)
| | - Chunqi Yang
- Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China; (J.C.); (Y.L.)
| | - Shihuang Pu
- Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China; (J.C.); (Y.L.)
| | - Jiancheng Wen
- Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China; (J.C.); (Y.L.)
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