119 results on '"Deng, Feng"'
Search Results
2. Exploring the Genetic Association of the ABAT Gene with Alzheimer’s Disease
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Min Xu, Quanzhen Zheng, Rui Bi, Yong-Gang Yao, Ya-Ping Lu, Liwen Tan, and Deng-Feng Zhang
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0301 basic medicine ,Genetics ,Neuroscience (miscellaneous) ,Genome-wide association study ,Single-nucleotide polymorphism ,Biology ,Transcriptome ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,030104 developmental biology ,0302 clinical medicine ,Neurology ,microRNA ,Expression quantitative trait loci ,GABAergic ,Gene ,030217 neurology & neurosurgery ,Genetic association - Abstract
Accumulating evidence demonstrated that GABAergic dysfunction contributes to the pathogenesis of Alzheimer’s disease (AD). The GABA aminotransferase (ABAT) gene encodes a mitochondrial GABA transaminase and plays key roles in the biogenesis and metabolism of gamma-aminobutyric acid (GABA), which is a major inhibitory neurotransmitter. In this study, we performed an integrative study at the genetic and expression levels to investigate the potential genetic association between the ABAT gene and AD. Through re-analyzing data from the currently largest meta-analysis of AD genome-wide association study (GWAS), we identified genetic variants in the 3’-UTR of ABAT as the top AD-associated SNPs (P
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- 2021
3. Notholirion campanulatum is co-specific with N. bulbuliferum (Liliaceae) based on morphology and molecular data
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Mei Yang, Xing-Jin He, Song-Dong Zhou, Deng-Feng Xie, and Juan Li
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Phylogenetic tree ,Notholirion ,Synonym ,Ovary (botany) ,Plant Science ,Biology ,medicine.disease_cause ,biology.organism_classification ,Tepal ,Chloroplast DNA ,Pollen ,Botany ,medicine ,Taxonomy (biology) ,Ecology, Evolution, Behavior and Systematics - Abstract
Notholirion campanulatum and N. bulbuliferum are parapatrically distributed in the Qinghai-Tibetan Plateau and adjacent regions, however, their relationship has been controversial for a long time. In this study, six morphological characters including colour of corolla/ovary/bulblet, corolla shape, tepal size, and pollen form, together with nuclear ITS and four cpDNA markers (matK, ndhA, ndhG-I, and petL-G) were selected to perform a comprehensive analysis on 23 populations. Our results indicate that morphological characters of N. campanulatum and N. bulbuliferum are congruent with each other, and the phylogenetic analysis revealed that N. campanulatum closely nested with N. bulbuliferum. Therefore, we propose that these two species should be regarded as synonyms.
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- 2020
4. Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences
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Xing-Jin He, Song-Dong Zhou, Deng-Feng Xie, Fu-Min Xie, Yan Yu, and Chuan Xie
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0106 biological sciences ,0301 basic medicine ,Article Subject ,Biology ,01 natural sciences ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Allium ,Evolution, Molecular ,03 medical and health sciences ,Genus ,Phylogenetics ,Botany ,Genome, Chloroplast ,Genome size ,Phylogeny ,Base Composition ,General Immunology and Microbiology ,Phylogenetic tree ,DNA, Chloroplast ,Sequence Analysis, DNA ,General Medicine ,biology.organism_classification ,030104 developmental biology ,Medicine ,Subgenus ,GC-content ,Research Article ,010606 plant biology & botany - Abstract
The section Pallasia is one of the components of the genus Allium subgenus Allium (Amaryllidaceae), and species relationship in this section is still not resolved very well, which hinders further evolutionary and adaptive studies. Here, the complete chloroplast genomes of five sect. Pallasia species were reported, and a comparative analysis was performed with other three related Allium species. The genome size of the eight species ranged from 151,672 bp to 153,339 bp in length, GC content changed from 36.7% to 36.8%, and 130 genes (except Allium pallasii), 37 tRNA, and 8 rRNA were identified in each genome. By analyzing the IR/LSC and IR/SSC boundary, A. pallasii exhibited differences compared with other seven species. Phylogenetic analysis achieved high supports in each branch, seven of the eight Allium species cluster into a group, and A. pallasii exhibit a close relationship with A. obliquum. Higher pairwise Ka/Ks ratios were found in A. schoenoprasoides compared to A. caeruleum and A. macrostemon while a lower value of Ka/Ks ratios was detected between A. caeruleum and A. macrostemon. This study will be a great contribution to the future phylogenetic and adaptive research in Allium.
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- 2020
5. Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences
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Yan Yu, Lin-Jian Gui, Dan-Mei Su, Song-Dong Zhou, Jin-Bo Tan, Deng-Feng Xie, and Xing-Jin He
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Phylogenetic tree ,Lineage (evolution) ,Amaryllidaceae ,food and beverages ,Sequence Analysis, DNA ,Original Articles ,Plant Science ,Biology ,biology.organism_classification ,Allium ,Evolution, Molecular ,Monophyly ,Genus ,Evolutionary biology ,Phylogenetics ,Subgenus ,Adaptation ,Genome, Chloroplast ,Phylogeny - Abstract
Background and AimsThe genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study.MethodsIn this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families.ResultsOur phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species.ConclusionsOur results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
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- 2020
6. Mesenchymal stem cell-derived exosomes ameliorate cardiomyocyte apoptosis in hypoxic conditions through microRNA144 by targeting the PTEN/AKT pathway
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Jingfeng Wang, Xiao-Lin Zhu, Deng-feng Geng, Yangxin Chen, Tao Wu, Zhuzhi Wen, and Zun Mai
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0301 basic medicine ,Medicine (miscellaneous) ,Apoptosis ,Transfection ,Exosomes ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Exosome ,Rats, Sprague-Dawley ,lcsh:Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Animals ,Humans ,PTEN ,Myocytes, Cardiac ,lcsh:QD415-436 ,Protein kinase B ,PI3K/AKT/mTOR pathway ,lcsh:R5-920 ,biology ,Chemistry ,Research ,PTEN/AKT pathway ,Mesenchymal stem cell ,microRNA-144 ,PTEN Phosphohydrolase ,Cell Biology ,Microvesicles ,Rats ,MicroRNAs ,030104 developmental biology ,030220 oncology & carcinogenesis ,Cancer research ,biology.protein ,Molecular Medicine ,Mesenchymal stem cells ,Cell apoptosis ,Stem cell ,lcsh:Medicine (General) ,Proto-Oncogene Proteins c-akt ,Signal Transduction - Abstract
Background A growing body of evidence suggests that stem cell-derived exosomal microRNAs (miRNAs) could be a promising cardioprotective therapy in the context of hypoxic conditions. The present study aims to explore how miRNA-144 (miR-144), a miRNA contained in bone marrow mesenchymal stem cell (MSC)-derived exosomes, exerts a cardioprotective effect on cardiomyocyte apoptosis in the context of hypoxic conditions and identify the underlying mechanisms. Methods MSCs were cultured using the whole bone marrow adherent method. MSC-derived exosomes were isolated using the total exosome isolation reagent and confirmed by nanoparticle trafficking analysis as well as western blotting using TSG101 and CD63 as markers. The hypoxic growth conditions for the H9C2 cells were established using the AnaeroPack method. Treatment conditions tested included H9C2 cells pre-incubated with exosomes, transfected with miR-144 mimics or inhibitor, or treated with the PTEN inhibitor SF1670, all under hypoxic growth conditions. Cell apoptosis was determined by flow cytometry using 7-ADD and Annexin V together. The expression levels of the miRNAs were detected by real-time PCR, and the expression levels of AKT/p-AKT, Bcl-2, caspase-3, HIF-1α, PTEN, and Rac-1 were measured by both real-time PCR and western blotting. Results Exosomes were readily internalized by H9C2 cells after co-incubation for 12 h. Exosome-mediated protection of H9C2 cells from apoptosis was accompanied by increasing levels of p-AKT. MiR-144 was found to be highly enriched in MSC-derived exosomes. Transfection of cells with a miR-144 inhibitor weakened exosome-mediated protection from apoptosis. Furthermore, treatment of cells grown in hypoxic conditions with miR-144 mimics resulted in decreased PTEN expression, increased p-AKT expression, and prevented H9C2 cell apoptosis, whereas treatment with a miR-144 inhibitor resulted in increased PTEN expression, decreased p-AKT expression, and enhanced H9C2 cell apoptosis in hypoxic conditions. We also validated that PTEN was a target of miR-144 by using luciferase reporter assay. Additionally, cells treated with SF1670, a PTEN-specific inhibitor, resulted in increased p-AKT expression and decreased H9C2 cell apoptosis. Conclusions These findings demonstrate that MSC-derived exosomes inhibit cell apoptotic injury in hypoxic conditions by delivering miR-144 to cells, where it targets the PTEN/AKT pathway. MSC-derived exosomes could be a promising therapeutic vehicle to facilitate delivery of miRNA therapies to ameliorate ischemic conditions.
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- 2020
7. Diversity of sugarcane root‐associated endophytic Bacillus and their activities in enhancing plant growth
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Yang-Rui Li, Zhuo-Xin Yu, Manoj Kumar Solanki, Yong-Xiu Xing, Li-Tao Yang, Deng‐Feng Dong, and Zhen Wang
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Siderophore ,Antifungal Agents ,Biological pest control ,Siderophores ,Bacillus ,Biomass ,engineering.material ,Plant Roots ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,Bacillus isolates ,Endophytes ,Colonization ,Plant Diseases ,030304 developmental biology ,0303 health sciences ,Genetic diversity ,Indoleacetic Acids ,biology ,030306 microbiology ,fungi ,Fungi ,Genetic Variation ,food and beverages ,Phosphorus ,General Medicine ,biology.organism_classification ,Saccharum ,Horticulture ,engineering ,Fertilizer ,Biotechnology - Abstract
Aims Plant tissues are the reservoirs of beneficial and harmful microbes that regulates plant growth. In the present study, we investigated the diversity, function and colonization of sugarcane roots associated with Bacillus spp. Methods and results A total of 20 Bacillus strains were isolated and identified by 16S rRNA gene sequencing, and their genetic diversity was examined by BOX, ERIC, REP, (GTG)5 PCR techniques. Among all Bacillus isolates, 65% showed indole acetic acid-like compounds production, 50% solubilized phosphorus and 25% of the isolates were able to secrete siderophore. Moreover, all 20 Bacillus isolates showed antifungal activity against eight fungal pathogens and 11 of them (55%) antagonized tomato grey mold. Based on the plant growth-promoting traits and antifungal potential, isolate Y8 was selected for root and plant tissue colonization assays and a greenhouse-level sugarcane growth promotion study. Fluorescence microscopy results confirmed that isolate Y8 has a strong ability to colonize in the sugarcane root and leaves, and the root surface association of Y8 was confirmed by scanning electron microscopy. Furthermore, greenhouse experimental results demonstrated that Y8 has a significant effect on enhancing sugarcane biomass and root length. Conclusions Endophytic Bacillus strains have growth-promoting properties and anti-fungal ability that can enhance plant fitness in an eco-friendly manner. Significance and impact of the study Endophytic Bacillus strains would be a potential alternative to chemical fertilizer as well as a biocontrol agent in the future.
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- 2019
8. A Combined Morphological and Molecular Evolutionary Analysis of Karst-Environment Adaptation for the Genus Urophysa (Ranunculaceae)
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Rui-Yu Cheng, Xiang-Yi Zhang, Xiao Fu, Yan-Ling Lan, Chang-Bao Wang, Xing-Jin He, Deng-Feng Xie, and Megan Price
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adaptive evolution ,Phylogenetic tree ,biology ,Aquilegia ,Urophysa ,Calcium ion transport ,Plant culture ,Plant Science ,biology.organism_classification ,Coalescent theory ,SB1-1110 ,Evolutionary biology ,positive selection ,Cellular ion homeostasis ,karst environment ,Adaptation ,Gene ,transcriptome ,Function (biology) ,Original Research - Abstract
The karst environment is characterized by low soil water content, periodic water deficiency, and poor nutrient availability, which provides an ideal natural laboratory for studying the adaptive evolution of its inhabitants. However, how species adapt to such a special karst environment remains poorly understood. Here, transcriptome sequences of two Urophysa species (Urophysa rockii and Urophysa henryi), which are Chinese endemics with karst-specific distribution, and allied species in Semiaquilegia and Aquilegia (living in non-karst habitat) were collected. Single-copy genes (SCGs) were extracted to perform the phylogenetic analysis using concatenation and coalescent methods. Positively selected genes (PSGs) and clusters of paralogous genes (Mul_genes) were detected and subsequently used to conduct gene function annotation. We filtered 2,271 SCGs and the coalescent analysis revealed that 1,930 SCGs shared the same tree topology, which was consistent with the topology detected from the concatenated tree. Total of 335 PSGs and 243 Mul_genes were detected, and many were enriched in stress and stimulus resistance, transmembrane transport, cellular ion homeostasis, calcium ion transport, calcium signaling regulation, and water retention. Both molecular and morphological evidences indicated that Urophysa species evolved complex strategies for adapting to hostile karst environments. Our findings will contribute to a new understanding of genetic and phenotypic adaptive mechanisms of karst adaptation in plants.
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- 2021
9. Activation of PPARA-mediated autophagy reduces Alzheimer disease-like pathology and cognitive decline in a murine model
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Jing Yang, Rongcan Luo, Li Guiyu, Hejiang Zhou, Deng-Feng Zhang, Min Xu, Ling-Yan Su, Yu Fan, Yong-Gang Yao, Qianjin Liu, Lu-Xiu Yang, and Jiali Li
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0301 basic medicine ,Amyloid beta ,Plaque, Amyloid ,Amyloid beta-Protein Precursor ,Mice ,03 medical and health sciences ,Sequestosome 1 ,Alzheimer Disease ,Autophagy ,PSEN1 ,Animals ,Humans ,Cognitive Dysfunction ,PPAR alpha ,education ,Molecular Biology ,Mechanistic target of rapamycin ,education.field_of_study ,Amyloid beta-Peptides ,030102 biochemistry & molecular biology ,biology ,Neurodegenerative Diseases ,Cell Biology ,BECN1 ,Cell biology ,Disease Models, Animal ,030104 developmental biology ,biology.protein ,TFEB ,Microglia ,Peroxisome proliferator-activated receptor alpha ,MAP1LC3B ,Research Paper - Abstract
Alzheimer disease (AD) is the most common neurodegenerative disease. An imbalance between the production and clearance of Aβ (amyloid beta) is considered to be actively involved in AD pathogenesis. Macroautophagy/autophagy is a major cellular pathway leading to the removal of aggregated proteins, and upregulation of autophagy represents a plausible therapeutic strategy to combat overproduction of neurotoxic Aβ. PPARA/PPARα (peroxisome proliferator activated receptor alpha) is a transcription factor that regulates genes involved in fatty acid metabolism and activates hepatic autophagy. We hypothesized that PPARA regulates autophagy in the nervous system and PPARA-mediated autophagy affects AD. We found that pharmacological activation of PPARA by the PPARA agonists gemfibrozil and Wy14643 induces autophagy in human microglia (HM) cells and U251 human glioma cells stably expressing the human APP (amyloid beta precursor protein) mutant (APP-p.M671L) and this effect is PPARA-dependent. Administration of PPARA agonists decreases amyloid pathology and reverses memory deficits and anxiety symptoms in APP-PSEN1ΔE9 mice. There is a reduced level of soluble Aβ and insoluble Aβ in hippocampus and cortex tissues from APP-PSEN1ΔE9 mice after treatment with either gemfibrozil or Wy14643, which promoted the recruitment of microglia and astrocytes to the vicinity of Aβ plaques and enhanced autophagosome biogenesis. These results indicated that PPARA is an important factor regulating autophagy in the clearance of Aβ and suggested gemfibrozil be assessed as a possible treatment for AD. Abbreviation: Aβ: amyloid beta; ACTB: actin beta; ADAM10: ADAM metallopeptidase domain 10; AD: Alzheimer disease; AIF1/IBA1: allograft inflammatory factor 1; ANOVA: analysis of variance; APOE: apolipoprotein E; APP: amyloid beta precursor protein; APP-PSEN1ΔE9: APPswe/PSEN1dE9; BAFA1: bafilomycin A(1); BDNF: brain derived neurotrophic factor; BECN1: beclin 1; CD68: CD68 molecule; CREB1: cAMP responsive element binding protein 1; DAPI: 4‘,6-diamidino-2-phenylindole; DLG4/PSD-95: discs large MAGUK scaffold protein 4; DMSO: dimethyl sulfoxide; ELISA: enzyme linked immunosorbent assay; FDA: U.S. Food and Drug Administration; FKBP5: FK506 binding protein 5; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; gemfibrozil: 5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid; GFAP: glial fibrillary acidic protein; GLI2/THP1: GLI family zinc finger 2; HM: human microglia; IL6: interleukin 6; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; NC: negative control; OQ: opposite quadrant; PPARA/PPARα, peroxisome proliferator activated receptor alpha; PSEN1/PS1: presenilin 1; SEM: standard error of the mean; SQSTM1: sequestosome 1; SYP: synaptophysin; TFEB: transcription factor EB; TNF/TNF-α: tumor necrosis factor; TQ: target quadrant; WT: wild type; Wy14643: 2-[4-chloro-6-(2,3-dimethylanilino)pyrimidin-2-yl]sulfanylacetic acid
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- 2019
10. Genetic Analyses of Alzheimer’s Disease in China: Achievements and Perspectives
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Rui Bi, Min Xu, Deng-Feng Zhang, and Yong-Gang Yao
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China ,Candidate gene ,Biomedical Research ,Physiology ,Cognitive Neuroscience ,Population ,Genome-wide association study ,Disease ,Biology ,Polymorphism, Single Nucleotide ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Alzheimer Disease ,Genetic linkage ,Animals ,Humans ,education ,030304 developmental biology ,Genetic association ,0303 health sciences ,education.field_of_study ,Cell Biology ,General Medicine ,Heritability ,Evolutionary biology ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
Since 2010, the Chinese have become one of the most aged populations in the world, leading to a severe burden of neurodegenerative disorders. Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and has a high genetic heritability. In the past two decades, numerous genetic analyses, from linkage analyses and candidate gene studies to genome-wide association studies (GWASs) and next-generation sequencing studies, have identified dozens of AD susceptibility or causal genes. These studies have provided a comprehensive genetic view and contributed to the understanding of the pathological and molecular mechanisms of the disease. However, most of the recognized AD genetic risk factors have been reported in studies based on European populations or populations of European ancestry, and data about the genetics of AD from other populations has been very limited. As China has the largest AD population in the world and because of the remarkable genetic differences between the East and the West, deciphering the genetic basis and molecular mechanism in Chinese patients with AD may add key points to the full characterization of AD. In this review, we present an overview of the current state of AD genetic research in China, with an emphasis on genome-level studies. We also describe the challenges and opportunities for future advances, especially for in-depth collaborations, brain bank construction, and primate animal modeling. There is an urgent need to promote public awareness and increase our collaborations and data sharing.
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- 2019
11. The effect of Hengduan Mountains Region (HMR) uplift to environmental changes in the HMR and its eastern adjacent area: Tracing the evolutionary history of Allium section Sikkimensia (Amaryllidaceae)
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Xian-Lin Guo, Qing Liu, Xing-Jin He, Yan Zhong, Song-Dong Zhou, Chuan Xie, and Deng-Feng Xie
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0106 biological sciences ,0301 basic medicine ,China ,Pleistocene ,Demographic history ,Species distribution ,Climate change ,Biology ,Late Miocene ,010603 evolutionary biology ,01 natural sciences ,Allium ,03 medical and health sciences ,Genetics ,Molecular Biology ,Ecosystem ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Isolation by distance ,Ecology ,DNA, Chloroplast ,Genetic Variation ,Last Glacial Maximum ,Biological Evolution ,Phylogeography ,030104 developmental biology ,Haplotypes ,Sample Size ,Genetic structure - Abstract
Exploring the effects of orographic events and climatic shifts on geographic distribution of organism in the Hengduan Mountains Region (HMR) and its eastern adjacent area is crucial to the understanding of the environmental changes to organismal evolution. To gain further insight into these processes, we reconstruct evolutionary history of ten species in Allium section Sikkimensia, distributed across regions abovementioned. Using chloroplast and nuclear sequence variation of 79 populations of these ten Allium species with known morphological preferences, we elucidate the phylogenetic relationship, divergence time, ancestral area and genetic structures. Climatic variables analysis, Isolation by distance (IBD) and environment (IBE) and Species distribution modeling (SDM) were analyzed along different genetic clades. These analyses indicated that the initial split of Sikkimensia was triggered by climate changes following Qinghai-Tibet Plateau sensu lato (QTPsl) uplift during the late Miocene. Subsequently, divergences within lineage (lineage A)/among lineages (lineage C and D) in Sikkimensia may be induced by the intense uplift of the HMR around 3–4 Ma and abrupt intensifying of the Asian monsoon regimes. Furthermore, Sikkimensia populations exhibited lopsided demographic history in the Last Glacial Maximum (LGM), as was indicated by the expansion of their range in the QDM and contraction in the HMR. Our findings appear to suggest that the HMR uplift could have strengthened the orographic difference between the HMR and its eastern adjacent area and led to a colder climate in the HMR, while geological topography also played an important role for taxa to respond the climate change that had taken place in the HMR and its eastern adjacent area during the Pleistocene.
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- 2019
12. Emericelactones A-D: Four novel polyketides produced by Emericella sp. XL 029, a fungus associated the leaves of Panax notoginseng
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Xue-Jiao Pang, Lu-Lin Xu, Deng-Feng Yang, Peng-Jie Xian, Wen-Ting Zhao, Xiao-Long Yang, Hai-Yan Fu, Yan-Duo Tao, Shuai-Bing Zhang, and Hai-Li Chen
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biology ,010405 organic chemistry ,Chemistry ,Stereochemistry ,Organic Chemistry ,Pathogenic bacteria ,Fungus ,010402 general chemistry ,biology.organism_classification ,Antimicrobial ,medicine.disease_cause ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Rhizoctonia solani ,Drug Discovery ,medicine ,Gibberella ,Epimer ,Panax notoginseng ,Verticillium dahliae - Abstract
The application of an OSMAC approach on an endophytic fungus Emericella sp. XL 029 has yielded four novel polyketides, emericelactones A-D (1–4). The structures and stereochemistry of 1–4 were elucidated by NMR and MS data analyses, computational methods, as well as by comparison with known compounds. Compound 1 contained an unprecedented linear pentaene substructure ending in an oxabicyclo[2.2.1]heptane moiety, while compounds 2–4 are epimers possessing an unprecedented linear triene structures ending in two cyclic moieties of an oxabicyclo[2.2.1]heptane and a cyclopentan-1-one. Compounds 1–4 showed moderate antimicrobial activities against three agricultural pathogenic fungi (Verticillium dahliae Kleb, Rhizoctonia solani and Gibberella saubinetii) and two human pathogenic bacteria (Micrococcus lysodeikticus and Salmonella typhi) with MIC values of 25–50 μg/mL.
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- 2018
13. Complement C7 is a novel risk gene for Alzheimer's disease in Han Chinese
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Deng-Feng Zhang, Xiong-Jian Luo, Yu Fan, Dong Wang, Chen Zhang, Min Xu, Ming Li, Guihong Wang, Yiru Fang, Tianzi Jiang, Li-Li Kong, Rongcan Luo, Guo-Dong Li, Jin Li, Hong-Yan Jiang, Rui Bi, Chunjiu Zhong, Hejiang Zhou, Yong-Gang Yao, Alzheimer's Disease Neuroimaging Initiative, Liwen Tan, Yong Wu, and Nengyin Sheng
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Multidisciplinary ,neuroimaging ,Mutant ,Wild type ,02 engineering and technology ,Disease ,Odds ratio ,Biology ,Alzheimer's disease ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,3. Good health ,0104 chemical sciences ,Complement system ,Immunology ,Biology & Biochemistry ,Missense mutation ,C7 ,whole-exome sequencing ,0210 nano-technology ,Gene ,Exome sequencing ,complement system ,Research Article - Abstract
Alzheimer's disease is the most common neurodegenerative disease, and has a high level of genetic heritability and population heterogeneity. In this study, we performed the whole-exome sequencing of Han Chinese patients with familial and/or early-onset Alzheimer's disease, followed by independent validation, imaging analysis and function characterization. We identified an exome-wide significant rare missense variant rs3792646 (p.K420Q) in the C7 gene in the discovery stage (P = 1.09 × 10−6, odds ratio = 7.853) and confirmed the association in different cohorts and a combined sample (1615 cases and 2832 controls, Pcombined = 2.99 × 10−7, odds ratio = 1.930). The risk allele was associated with decreased hippocampal volume and poorer working memory performance in early adulthood, thus resulting in an earlier age of disease onset. Overexpression of the mutant p.K420Q disturbed cell viability, immune activation and β-amyloid processing. Electrophysiological analyses showed that the mutant p.K420Q impairs the inhibitory effect of wild type C7 on the excitatory synaptic transmission in pyramidal neurons. These findings suggested that C7 is a novel risk gene for Alzheimer's disease in Han Chinese.
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- 2018
14. Characterization of the complete chloroplast genome of
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Fang-Yu Jin, Song-Dong Zhou, Deng-Feng Xie, and Xing-Jin He
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0301 basic medicine ,Genetics ,phylogenetic analysis ,food and beverages ,Allium prattii ,Biology ,biology.organism_classification ,Genome ,DNA sequencing ,Chloroplast ,03 medical and health sciences ,030104 developmental biology ,complete chloroplast genome ,Allium kingdonii ,Endemism ,Molecular Biology ,Mitogenome Announcement ,Research Article - Abstract
The genus Allium is one of the world’s largest monocot genera. However, few reports on the complete chloroplast genome of Allium plants are reported. In this study, we reported the complete chloroplast genome of Allium prattii. The genome sequence was 154,482 bp in length, including a large single copy region (LSC) of 83,392 bp and a small single copy region (SSC) of 18,064 bp, which were separated by two inverted repeat (IR) regions of 26,513 bp. The complete chloroplast genome contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with several reported chloroplast genomes showed that A. prattii has a close genetic relationship with A. cepa and A. sativum.
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- 2021
15. Mapping leprosy-associated coding variants of interleukin genes by targeted sequencing
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Deng-Feng Zhang, Yu-Ye Li, Hui-Long Li, Quanzhen Zheng, Dong Wang, Guo-Ping Zhu, Yong-Gang Yao, Rui Bi, and Min Xu
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0301 basic medicine ,Male ,China ,030105 genetics & heredity ,Biology ,Polymorphism, Single Nucleotide ,Deep sequencing ,DNA sequencing ,03 medical and health sciences ,Asian People ,Leprosy ,Genetics ,medicine ,Genetic predisposition ,Coding region ,Humans ,Genetic Predisposition to Disease ,RNA, Messenger ,Genotyping ,Gene ,Genetics (clinical) ,Interleukins ,Interleukin ,Middle Aged ,medicine.disease ,030104 developmental biology ,Case-Control Studies ,Immunology ,Female - Abstract
Previous genotyping-based assays have identified non-coding variants of several interleukins (ILs) being associated with genetic susceptibility to leprosy. However, understanding of the involvement of coding variants within all IL family genes in leprosy was still limited. To obtain the full mutation spectrum of all ILs in leprosy, we performed a targeted deep sequencing of coding regions of 58 ILs genes in 798 leprosy patients (age 56.2 ± 14.4; female 31.5%) and 990 healthy controls (age 38.1 ± 14.0; female 44.3%) from Yunnan, Southwest China. mRNA expression alterations of ILs in leprosy skin lesions or in response to M. leprae treatment were estimated by using publicly available expression datasets. Two coding variants in IL27 (rs17855750, p.S59A, p = 4.02 × 10-8 , odds ratio [OR] = 1.748) and IL1RN (rs45507693, p.A106T, p = 1.45 × 10-5 , OR = 3.629) were significantly associated with leprosy risk. mRNA levels of IL27 and IL1RN were upregulated in whole blood cells after M. leprae stimulation. These data showed that IL27 and IL1RN are leprosy risk genes. Further functional study is required for characterizing the exact role of ILs in leprosy.
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- 2021
16. Author response for 'Mapping leprosy‐associated coding variants of interleukin genes by targeted sequencing'
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Hui-Long Li, Yong-Gang Yao, Guo-Ping Zhu, Min Xu, Rui Bi, Dong Wang, Quanzhen Zheng, Yu-Ye Li, and Deng-Feng Zhang
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Genetics ,medicine ,Interleukin ,Leprosy ,Biology ,medicine.disease ,Gene ,Coding (social sciences) - Published
- 2021
17. Phylogeny and Comparative Analysis for the Plastid Genomes of Five Tulipa (Liliaceae)
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Xin-Fen Gao, Xing-Jin He, Zhen Zhang, Song-Dong Zhou, Juan Li, Deng-Feng Xie, Yan Yu, Dan-Mei Su, and Megan Price
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0106 biological sciences ,0301 basic medicine ,Comparative genomics ,education.field_of_study ,General Immunology and Microbiology ,Phylogenetic tree ,Article Subject ,Population ,General Medicine ,Biology ,01 natural sciences ,Genome ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Monophyly ,030104 developmental biology ,Phylogenetics ,Evolutionary biology ,Phylogenomics ,Medicine ,Plastid ,education ,010606 plant biology & botany - Abstract
Species of Tulipa (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary diversity centres of Tulipa, but the molecular studies of Tulipa species from this location are lacking. In our study, we assembled four Tulipa plastid genomes from the Tien Shan Mountains, T. altaica, T. iliensis, T. patens, and T. thianschanica, combined with the plastid genome of T. sylvestris to compare against other Liliaceae plastid genomes. We focussed on the species diversity and evolution of their plastid genomes. The five Tulipa plastid genomes proved highly similar in overall size (151,691–152,088 bp), structure, gene order, and content. With comparative analysis, we chose 7 mononucleotide SSRs from the Tulipa species that could be used in further population studies. Phylogenetic analyses based on 24 plastid genomes robustly supported the monophyly of Tulipa and the sister relationship between Tulipa and Amana, Erythronium. T. iliensis, T. thianschanica, and T. altaica were clustered together, and T. patens was clustered with T. sylvestris, with our results clearly demonstrating the relationships between these five Tulipa species. Our results provide a more comprehensive understanding of the phylogenomics and comparative genomics of Tulipa.
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- 2021
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18. Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships
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Xing-Jin He, Jun Wen, Deng-Feng Xie, Zi-Xuan Li, Ling-Jian Gui, Chang Peng, and Ting Ren
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0106 biological sciences ,0301 basic medicine ,Genome evolution ,Genotype ,Evolution ,Characterization ,Genome, Plastid ,Plant Science ,Biology ,Genes, Plant ,01 natural sciences ,Coalescent theory ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,lcsh:Botany ,Ligusticum ,Internal transcribed spacer ,Genome size ,Phylogeny ,Phylogenetic tree ,Genetic Variation ,Sequence Analysis, DNA ,Plastome ,biology.organism_classification ,Relaxed selection ,lcsh:QK1-989 ,030104 developmental biology ,Chloroplast DNA ,Evolutionary biology ,Phylogenetic relationships ,Research Article ,010606 plant biology & botany - Abstract
Background The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. Results Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. Conclusion The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.
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- 2020
19. A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae)
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Chang Peng, Jun Wen, Xing-Jin He, Qing Liu, Yan Yu, Deng-Feng Xie, and Song-Dong Zhou
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Subfamily ,Phylogenetic tree ,Fossils ,Plant Science ,Acronema ,Original Articles ,Biology ,Tribe (biology) ,biology.organism_classification ,Coalescent theory ,Evolution, Molecular ,Sister group ,Evolutionary biology ,Phylogenetics ,Clade ,Transcriptome ,Phylogeny ,Apiaceae - Abstract
Background and AimsA long-standing controversy in the subfamily Apioideae concerns relationships among the major lineages, which has prevented a comprehensive study of their fruits and evolutionary history. Here we use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae.MethodsIn total, 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Fruit morphology and anatomy were studied in combination with the species tree. Eleven SCGs were screened out for dating analysis with two fossils selected for calibration.Key ResultsA well-supported species tree was generated with a topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] that differed from previous trees. Daucinae and Torilidinae were not in the tribe Scandiceae and existed as sister groups to the Acronema Clade. Five branches (I–V) of the species tree showed low quartet support but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Mya (95 % highest posterior density interval, 45.18–73.53 Mya).ConclusionsThis study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimation methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of Apioideae might have evolved in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggests that Daucinae and Torilidinae should be restored to the tribe level. Our results provide new insights into the morphological evolution of this subfamily, which may contribute to a better understanding of species diversification in Apioideae. Molecular dating analysis suggests that uplift of the Qinghai–Tibetan Plateau (QTP) and climate changes probably drove rapid speciation and diversification of Apioideae in the QTP region.
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- 2020
20. Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
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Yan Yu, Xing-Jin He, Deng-Feng Xie, Song-Dong Zhou, Jun-Pei Chen, and Xin Yang
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0106 biological sciences ,0301 basic medicine ,General Immunology and Microbiology ,Phylogenetic tree ,Article Subject ,General Medicine ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Monophyly ,030104 developmental biology ,Chloroplast DNA ,Evolutionary biology ,Molecular phylogenetics ,Medicine ,Subgenus ,Genome size ,NdhF - Abstract
Recent advances in molecular phylogenetics provide us with information of Allium L. taxonomy and evolution, such as the subgenus Cyathophora, which is monophyletic and contains five species. However, previous studies detected distinct incongruence between the nrDNA and cpDNA phylogenies, and the interspecies relationships of this subgenus need to be furtherly resolved. In our study, we newly assembled the whole chloroplast genome of four species in subgenus Cyathophora and two allied Allium species. The complete cp genomes were found to possess a quadripartite structure, and the genome size ranged from 152,913 to 154,174 bp. Among these cp genomes, there were subtle differences in the gene order, gene content, and GC content. Seven hotspot regions (infA, rps16, rps15, ndhF, trnG-UCC, trnC-GCA, and trnK-UUU) with nucleotide diversity greater than 0.02 were discovered. The selection analysis showed that some genes have elevated Ka/Ks ratios. Phylogenetic analysis depended on the complete chloroplast genome (CCG), and the intergenic spacer regions (IGS) and coding DNA sequences (CDS) showed same topologies with high support, which revealed that subgenus Cyathophora was a monophyletic group, containing four species, and A. cyathophorum var. farreri was sister to A. spicatum with 100% bootstrap value. Our study revealed selective pressure may exert effect on several genes of the six Allium species, which may be useful for them to adapt to their specific living environment. We have well resolved the phylogenetic relationship of species in the subgenus Cyathophora, which will contribute to future evolutionary studies or phylogeographic analysis of Allium.
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- 2020
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21. Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution
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Jiao Huang, Yan-Mei Liu, Xing-Jin He, Deng-Feng Xie, Song-Dong Zhou, and Yan Yu
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0106 biological sciences ,0301 basic medicine ,fritillaria ,Fritillaria ,Plant Science ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,genome structure ,03 medical and health sciences ,Liliales ,Phylogenomics ,Liliaceae ,Ecology, Evolution, Behavior and Systematics ,Ecology ,biology ,Phylogenetic tree ,Botany ,Cardiocrinum ,phylogenomics ,biology.organism_classification ,030104 developmental biology ,Chloroplast DNA ,Evolutionary biology ,QK1-989 ,plastome genome - Abstract
Fritillaria is a genus that has important medicinal and horticultural values. The study involved the most comprehensive chloroplast genome samples referring to Old and New World clades of Fritillaria for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome sequences of Fritillaria which proved highly similar in overall size (151,652&ndash, 152,434 bp), genome structure, gene content, and order. Comparing them with other species of Liliales (6 out of 10 families) indicated the same similarity but showed some structural variations due to the contraction or expansion of the inverted repeat (IR) regions. A/T mononucleotides, palindromic, and forward repeats were the most common types. Six hypervariable regions (rps16-trnQ, rbcL-accD, accD-psaI, psaJ-rpl33, petD-rpoA, and rpl32-trnL) were discovered based on 26 Fritillaria whole-plastomes to be potential molecular markers. Based on the plastome data that were collected from 26 Fritillaria and 21 Lilium species, a phylogenomic study was carried out with three Cardiocrinum species as outgroups. Fritillaria was sister to Lilium with a high support value, and the interspecies relationships within subgenus Fritillaria were resolved very well. The six hypervariable regions can be used as candidate DNA barcodes of Fritillaria and the phylogenomic framework can guide extensive genomic sampling for further phylogenetic analyses.
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- 2020
22. (±)-Preisomide: A new alkaloid featuring a rare naturally occurring tetrahydro-2H-1,2-oxazin skeleton from an endophytic fungus Preussia isomera by using OSMAC strategy
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Heng-Ye Chen, Hai-Li Chen, Wen-Ting Zhao, Deng-Feng Yang, Qingpei Liu, Wei Zhao, and Xiao-Long Yang
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Pharmacology ,Preussia isomera ,biology ,010405 organic chemistry ,Chemistry ,Stereochemistry ,Alkaloid ,Panax notoginseng ,General Medicine ,medicine.disease_cause ,biology.organism_classification ,01 natural sciences ,Enterococcus faecalis ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,Alkaloids ,Ascomycota ,Staphylococcus aureus ,Drug Discovery ,medicine ,Endophytes ,Gibberella ,Antibacterial activity ,Enterococcus faecium - Abstract
A new alkaloid, named (±)-preisomide (1), together with five known polyketides (2–6), were isolated from an endophytic fungus Preussia isomera in Panax notoginseng by using one strain-many compounds (OSMAC) strategy. Their structures were identified by extensive spectroscopic experiments and comparison with literature data. Structurally, compound 1 possessed a rare naturally occurring tetrahydro-2H-1,2-oxazin ring. Compound 6 displayed significant antibacterial activity against multidrug-resistant Enterococcus faecium, methicinllin-resistant Staphylococcus aureus and multidrug-resistant Enterococcus faecalis with an MIC value of 25 μg/mL, as well as moderate antifungal activity against Gibberella saubinetii with an MIC value of 50 μg/mL.
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- 2019
23. Genetic association of the cytochrome c oxidase-related genes with Alzheimer’s disease in Han Chinese
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Hong-Yan Jiang, Tao Li, Deng-Feng Zhang, Rui Bi, Yiru Fang, Min Xu, Qiu-Xiang Hu, Yu Fan, Liwen Tan, Wen Zhang, Yong-Gang Yao, and Chen Zhang
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Male ,0301 basic medicine ,Mice, Transgenic ,Polymorphism, Single Nucleotide ,Article ,Electron Transport Complex IV ,03 medical and health sciences ,NDUFA4 ,Asian People ,Alzheimer Disease ,medicine ,Animals ,Humans ,Cytochrome c oxidase ,SURF1 ,Genetic Association Studies ,Aged ,COX6B2 ,Genetic association ,Aged, 80 and over ,Pharmacology ,Genetics ,biology ,Genetic Variation ,COX5A ,medicine.disease ,Psychiatry and Mental health ,030104 developmental biology ,Case-Control Studies ,Expression quantitative trait loci ,biology.protein ,Female ,Alzheimer's disease - Abstract
Alzheimer’s disease (AD) is the most common cause of dementia. Mitochondrial dysfunction has been widely reported in AD due to its important role in cellular metabolism and energy production. Complex IV (cytochrome c oxidase, COX) of mitochondrial electron transport chain, is particularly vulnerable in AD. Defects of COX in AD have been well documented, but there is little evidence to support the genetic association of the COX-related genes with AD. In this study, we investigated the genetic association between 17 nuclear-encoded COX-related genes and AD in 1572 Han Chinese. The whole exons of these genes were also screened in 107 unrelated AD patients with a high probability of hereditarily transmitted AD. Variants in COX6B1, NDUFA4, SURF1, and COX10 were identified to be associated with AD. An integrative analysis with data of eQTL, expression and pathology revealed that most of the COX-related genes were significantly downregulated in AD patients and mouse models, and the AD-associated variants in COX6B1, SURF1, and COX10 were linked to altered mRNA levels in brain tissues. Furthermore, mRNA levels of Ndufa4, Cox5a, Cox10, Cox6b2, Cox7a2, and Lrpprc were significantly correlated with Aβ plaque burden in hippocampus of AD mice. Convergent functional genomics analysis revealed strong supportive evidence for the roles of COX6B1, COX10, NDUFA4, and SURF1 in AD. As the result of our comprehensive analysis of the COX-related genes at the genetic, expression, and pathology levels, we have been able to provide a systematic view for understanding the relationships of the COX-related genes in the pathology of AD.
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- 2018
24. KHDC3L mutation causes recurrent pregnancy loss by inducing genomic instability of human early embryonic cells
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Ping Zheng, Lu Liu, Deng-Feng Zhang, Zhongliang Chen, Zhengyuan Xie, Bo Zhao, Weidao Zhang, and Yong-Gang Yao
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0301 basic medicine ,Genome instability ,Embryology ,Cellular differentiation ,Maternal Health ,Human Embryonic Stem Cells ,Poly (ADP-Ribose) Polymerase-1 ,Apoptosis ,Ataxia Telangiectasia Mutated Proteins ,Mice, SCID ,medicine.disease_cause ,Biochemistry ,Mice ,0302 clinical medicine ,PARP1 ,Pregnancy ,Medicine and Health Sciences ,Biology (General) ,Post-Translational Modification ,Phosphorylation ,Cells, Cultured ,Gene Editing ,Mutation ,Mammalian Genomics ,Cell Death ,General Neuroscience ,Obstetrics and Gynecology ,Genomics ,Nucleic acids ,Deletion Mutation ,Cell Processes ,Female ,General Agricultural and Biological Sciences ,Research Article ,Signal Transduction ,Abortion, Habitual ,QH301-705.5 ,DNA damage ,DNA repair ,Karyotype ,Biology ,DNA replication ,General Biochemistry, Genetics and Molecular Biology ,Genomic Instability ,03 medical and health sciences ,medicine ,Genetics ,Animals ,Humans ,Micronuclei, Chromosome-Defective ,General Immunology and Microbiology ,Embryos ,Biology and Life Sciences ,Proteins ,Recombinational DNA Repair ,DNA ,Cell Biology ,Embryo, Mammalian ,KH domain ,030104 developmental biology ,Gene Expression Regulation ,Animal Genomics ,Cancer research ,Women's Health ,CRISPR-Cas Systems ,Homologous recombination ,030217 neurology & neurosurgery ,Developmental Biology ,DNA Damage - Abstract
Recurrent pregnancy loss (RPL) is an important complication in reproductive health. About 50% of RPL cases are unexplained, and understanding the genetic basis is essential for its diagnosis and prognosis. Herein, we report causal KH domain containing 3 like (KHDC3L) mutations in RPL. KHDC3L is expressed in human epiblast cells and ensures their genome stability and viability. Mechanistically, KHDC3L binds to poly(ADP-ribose) polymerase 1 (PARP1) to stimulate its activity. In response to DNA damage, KHDC3L also localizes to DNA damage sites and facilitates homologous recombination (HR)-mediated DNA repair. KHDC3L dysfunction causes PARP1 inhibition and HR repair deficiency, which is synthetically lethal. Notably, we identified two critical residues, Thr145 and Thr156, whose phosphorylation by Ataxia-telangiectasia mutated (ATM) is essential for KHDC3L’s functions. Importantly, two deletions of KHDC3L (p.E150_V160del and p.E150_V172del) were detected in female RPL patients, both of which harbor a common loss of Thr156 and are impaired in PARP1 activation and HR repair. In summary, our study reveals both KHDC3L as a new RPL risk gene and its critical function in DNA damage repair pathways., Recurrent pregnancy loss is an important complication in reproductive health, and about 50% of cases remain unexplained. This study shows that KHDC3L safeguards the genomic stability of human early embryonic cells, and damaging mutations in its gene cause recurrent pregnancy loss in humans.
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- 2019
25. Missense Variants in HIF1A and LACC1 Contribute to Leprosy Risk in Han Chinese
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Dong Wang, Deng-Feng Zhang, Yu-Ye Li, Yong Wu, Xiu-Feng Yu, Rui Bi, Yu Fan, Yong-Gang Yao, Heng Long, Mahadev Malhi, and Min Xu
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Adult ,Male ,0301 basic medicine ,Adolescent ,Population ,Mutation, Missense ,Genome-wide association study ,Biology ,Polymorphism, Single Nucleotide ,Article ,Cohort Studies ,Young Adult ,03 medical and health sciences ,Asian People ,Risk Factors ,Genetic linkage ,Leprosy ,Exome Sequencing ,Ethnicity ,Genetics ,medicine ,Humans ,Missense mutation ,Genetic Predisposition to Disease ,RNA, Messenger ,Child ,education ,Alleles ,Genetics (clinical) ,Exome sequencing ,Aged ,Genetic association ,Aged, 80 and over ,education.field_of_study ,Intracellular Signaling Peptides and Proteins ,High-Throughput Nucleotide Sequencing ,Nuclear Proteins ,Proteins ,Reproducibility of Results ,Odds ratio ,Middle Aged ,Hypoxia-Inducible Factor 1, alpha Subunit ,medicine.disease ,Up-Regulation ,030104 developmental biology ,Trans-Activators ,Female - Abstract
Genome-wide association studies (GWASs) and genome-wide linkage studies (GWLSs) have identified numerous risk genes affecting the susceptibility to leprosy. However, most of the reported GWAS hits are noncoding variants and account for only part of the estimated heritability for this disease. In order to identify additional risk genes and map the potentially functional variants within the GWAS loci, we performed a three-stage study combining whole-exome sequencing (WES; discovery stage), targeted next-generation sequencing (NGS; screening stage), and refined validation of risk missense variants in 1,433 individuals with leprosy and 1,625 healthy control individuals from Yunnan Province, Southwest China. We identified and validated a rare damaging variant, rs142179458 (c.1045G>A [p.Asp349Asn]) in HIF1A, as contributing to leprosy risk (p = 4.95 × 10−9, odds ratio [OR] = 2.266). We were able to show that affected individuals harboring the risk allele presented with multibacillary leprosy at an earlier age (p = 0.025). We also confirmed the association between missense variant rs3764147 (c.760A>G [p.Ile254Val]) in the GWAS hit LACC1 (formerly C13orf31) and leprosy (p = 6.11 × 10−18, OR = 1.605). By using the population attributable fraction, we have shown that HIF1A and LACC1 are the major genes with missense variants contributing to leprosy risk in our study groups. Consistently, mRNA expression levels of both HIF1A and LACC1 were upregulated in the skin lesions of individuals with leprosy and in Mycobacterium leprae-stimulated cells, indicating an active role of HIF1A and LACC1 in leprosy pathogenesis.
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- 2018
26. Photochemical property of a Ru(<scp>ii</scp>) compound based on 3-(2-pyridyl)pyrazole and 2,2′-bipyridine for ablation of cancer cells
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Gao-Wen Yang, Lei Shen, Jie Yang, Guang Ming Li, Xin Zhang, Qiao-Yun Li, Dian Yu Chen, and Deng Feng Zou
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biology ,010405 organic chemistry ,medicine.medical_treatment ,Photodynamic therapy ,General Chemistry ,Enhanced permeability and retention effect ,Pyrazole ,010402 general chemistry ,biology.organism_classification ,01 natural sciences ,Catalysis ,0104 chemical sciences ,HeLa ,chemistry.chemical_compound ,chemistry ,In vivo ,Cancer cell ,Toxicity ,Materials Chemistry ,medicine ,Phototoxicity ,Nuclear chemistry - Abstract
Ru(II) compounds are potential candidates for photodynamic therapy (PDT). In the present study, a Ru(II) compound based on 3-(2-pyridyl)pyrazole (Hpypz) and 2,2′-bipyridine has been prepared and characterized. This compound can self-assemble to form nanoparticles (NPs) by nanoprecipitation in distilled water. These NPs with a mean size of 92 nm have good passive targeting by enhanced permeability and retention effect (EPR). In vitro studies on HeLa cells show that these NPs have high phototoxicity and a low IC50 (half-maximal inhibitory concentration) of only 8 μg mL−1 (12 μM), but they also have negligible dark toxicity. Moreover, such NPs can inhibit the migration of HeLa cells, indicating their potential to interfere with the transfer of tumors in vivo. Furthermore, in vivo investigations on nude mice demonstrate that such NPs can effectively inhibit the growth of the tumor. After treatment for 10 cycles, an obvious decrease in the tumor volume can be observed and in addition, the main organs (heart, liver, spleen, lung and kidney) suffer no damage, which indicates the high phototoxicity, low toxicity and excellent biocompatibility of these NPs.
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- 2018
27. The mtDNA replication-related genes TFAM and POLG are associated with leprosy in Han Chinese from Southwest China
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Guo-Dong Li, Heng Long, Yong-Gang Yao, Yu-Ye Li, Yu Fan, Xiu-Feng Yu, Deng-Feng Zhang, Dong Wang, and Rui Bi
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Adult ,DNA Replication ,Male ,0301 basic medicine ,China ,Mitochondrial DNA ,Adolescent ,DNA Copy Number Variations ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Dermatology ,Biology ,DNA, Mitochondrial ,Polymorphism, Single Nucleotide ,Biochemistry ,Mitochondrial Proteins ,Young Adult ,03 medical and health sciences ,Exon ,Asian People ,Humans ,Genetic Predisposition to Disease ,RNA, Messenger ,Child ,Molecular Biology ,Gene ,Mycobacterium leprae ,Genetic Association Studies ,Aged ,Skin ,Genetic association ,Aged, 80 and over ,Genetics ,High-Throughput Nucleotide Sequencing ,Exons ,Sequence Analysis, DNA ,Middle Aged ,TFAM ,biology.organism_classification ,DNA Polymerase gamma ,DNA-Binding Proteins ,030104 developmental biology ,Case-Control Studies ,Leprosy, Multibacillary ,Expression quantitative trait loci ,Female ,Leprosy, Paucibacillary ,Transcription Factors - Abstract
Background The pathogen Mycobacterium leprae of leprosy is heavily dependent on the host energy metabolites and nutritional products for survival. Previously we and others have identified associations of several mitochondrion-related genes and mitochondrial DNA (mtDNA) copy number alterations with leprosy and/or its subtype. We hypothesized that genetic variants of mtDNA replication-related genes would affect leprosy. Objective We aimed to identify genetic associations between the mtDNA replication-related genes TFAM, POLG and leprosy. Methods Genetic association study was performed in 2898 individuals from two independent sample sets in Yunnan Province, China. We first screened 7 tag SNPs of TFAM and POLG in 527 leprosy cases and 583 controls (Sample I). Expression quantitative trait loci (eQTL) analysis and differential mRNA expression were analyzed to discern potential effect of risk variants. The entire exon region of TFAM and POLG were further analyzed in 798 leprosy cases and 990 controls (Sample II; 4327 East Asians from the ExAC dataset was included as a reference control) by using targeted gene sequencing for fine mapping potentially causal variants. Results Two tag SNPs of TFAM (rs1049432, P = 0.007) and POLG (rs3176238, P = 0.006) were associated with multibacillary leprosy (MB) in Sample I and the significance survived correction for multiple comparisons. SNPs rs1937 of TFAM (which was linked with rs1049432) and rs61756401 of POLG were associated with leprosy, whereas no potentially causative coding variants were identified in Sample II. The eQTL analysis showed that rs1049432 was a significant cis eQTL for TFAM in nerve tissue (P = 1.20 × 10−12), and rs3176238 was a significant cis eQTL for POLG in nerve (P = 3.90 × 10−13) and skin tissues (P = 2.50 × 10−11). Consistently, mRNA level of POLG was differentially expressed in leprotic skin lesions. Conclusions Genetic variants of TFAM and POLG were associated with leprosy in Han Chinese, presumably by affecting gene expression.
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- 2017
28. Backbone phylogeny and evolution of Apioideae (Apiaceae): New insights from phylogenomic analyses of plastome data
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Ting Ren, Xian-Lin Guo, Deng-Feng Xie, Jun Wen, Megan Price, Ling-Jian Gui, Xing-Jin He, and Yi-Qi Deng
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0106 biological sciences ,0301 basic medicine ,Chloroplast capture ,Phylogenetic tree ,Context (language use) ,Sequence Analysis, DNA ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Coalescent theory ,Evolution, Molecular ,03 medical and health sciences ,030104 developmental biology ,Chloroplast DNA ,Phylogenetics ,Evolutionary biology ,Genetics ,Plastids ,Genome, Chloroplast ,Molecular clock ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Apiaceae - Abstract
Traditional phylogenies inferred from chloroplast DNA fragments have not obtained a well‐resolved evolutionary history for the backbone of Apioideae, the largest subfamily of Apiaceae. In this study, we applied the genome skimming approach of next‐generation sequencing to address whether the lack of resolution at the tip of the Apioideae phylogenetic tree is due to limited information loci or the footprint of ancient radiation. A total of 90 complete chloroplast genomes (including 23 newly sequenced genomes and covering 20 major clades of Apioideae) were analyzed (RAxML and MrBayes) to provide a phylogenomic reconstruction of Apioideae. Dating analysis was also implemented using BEAST to estimate the origin and divergence time of the major clades. As a result, the early divergences of Apioideae have been clarified but the relationship among its distally branching clades (Group A) was only partially resolved, with short internal branches pointing to an ancient radiation scenario. Four major clades, Tordyliinae I, Pimpinelleae I, Apieae and Coriandreae, were hypothesized to have originated from chloroplast capture events induced by early hybridization according to the incongruence between chloroplast-based and nrDNA-based phylogenetic trees. Furthermore, the variable and nested distribution of junction positions of LSC (Large single copy region) and IRB (inverted repeat region B) in Group A may reflect incomplete lineage sorting within this group, which possibly contributed to the unclear phylogenetic relationships among these clades inferred from plastome data. Molecular clock analysis revealed the chloroplast capture events mainly occurred during the middle to late Miocene, providing a geological and climate context for the evolution of Apioideae.
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- 2021
29. A systematic integrated analysis of brain expression profiles reveals YAP1 and other prioritized hub genes as important upstream regulators in Alzheimer's disease
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Yong Wu, Yong-Gang Yao, Min Xu, Deng-Feng Zhang, Hejiang Zhou, Rongcan Luo, Li-Li Kong, and Rui Bi
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Male ,0301 basic medicine ,Hub genes ,Epidemiology ,Regulator ,Gene Expression ,Disease ,Biology ,Transcriptome ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Developmental Neuroscience ,Alzheimer Disease ,Databases, Genetic ,Humans ,Gene Regulatory Networks ,Gene ,Adaptor Proteins, Signal Transducing ,YAP1 ,Health Policy ,Disease progression ,Brain ,YAP-Signaling Proteins ,Genomics ,Phosphoproteins ,Psychiatry and Mental health ,Brain expression ,030104 developmental biology ,Disease Progression ,Female ,Neurology (clinical) ,Geriatrics and Gerontology ,Neuroscience ,Transcription Factors - Abstract
Introduction Profiling the spatial-temporal expression pattern and characterizing the regulatory networks of brain tissues are vital for understanding the pathophysiology of Alzheimer's disease (AD). Methods We performed a systematic integrated analysis of expression profiles of AD-affected brain tissues (684 AD and 562 controls). A network-based convergent functional genomic approach was used to prioritize possible regulator genes during AD development, followed by functional characterization. Results We generated a complete list of differentially expressed genes and hub genes of the transcriptomic network in AD brain and constructed a Web server (www.alzdata.org) for public access. Seventeen hub genes active at the early stages, especially YAP1 , were recognized as upstream regulators of the AD network. Cellular assays proved that early alteration of YAP1 could promote AD by influencing the whole transcriptional network. Discussion Early expression disturbance of hub genes is an important feature of AD development, and interfering with this process may reverse the disease progression.
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- 2017
30. Whole-genome sequencing of monozygotic twins discordant for schizophrenia indicates multiple genetic risk factors for schizophrenia
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Chuanyue Wang, Qun Xiang, Ying He, Yong-Gang Yao, Ya Wang, Xiaogang Chen, Jinsong Tang, Yu Fan, Zongchang Li, Hong Li, Fengyu Zhang, Deng Feng Zhang, Raymond C.K. Chan, Fan He, Chunyu Liu, Yanqing Tang, Yanhui Liao, and Yin Yao Shugart
- Subjects
Adult ,Male ,0301 basic medicine ,Candidate gene ,DNA Copy Number Variations ,Schizophrenia (object-oriented programming) ,Monozygotic twin ,Biology ,medicine.disease_cause ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,mental disorders ,Genetics ,medicine ,Humans ,Missense mutation ,Genetic Predisposition to Disease ,Copy-number variation ,Allele ,Molecular Biology ,Mutation ,Whole Genome Sequencing ,Twins, Monozygotic ,Genetic architecture ,Pedigree ,Reelin Protein ,030104 developmental biology ,Schizophrenia ,Female - Abstract
Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight non-synonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p. V24689I mutation in TTN, p. S2506T mutation in GCN1L1, IVS3+1G > T in DOCK1) or had a benign to damaging effect according to in silico prediction analysis. By searching the inherited rare damaging or loss-of-function (LOF) variants and common susceptible alleles from three classes of schizophrenia candidate genes, we were able to distill genetic alterations in several schizophrenia risk genes, including GAD1, PLXNA2, RELN and FEZ1. Four inherited copy number variations (CNVs; including a large deletion at 16p13.11) implicated for schizophrenia were identified in four families, respectively. Most of families carried both missense DNMs and inherited risk variants, which might suggest that DNMs, inherited rare damaging variants and common risk alleles together conferred to schizophrenia susceptibility. Our results support that schizophrenia is caused by a combination of multiple genetic factors, with each DNM/variant showing a relatively small effect size. Copyright (C) 2017, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. All rights reserved.
- Published
- 2017
31. EGb 761 Protects Cardiac Microvascular Endothelial Cells against Hypoxia/Reoxygenation Injury and Exerts Inhibitory Effect on the ATM Pathway
- Author
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Dong Han, Zhuang Zhang, Chao Zhang, Kan Yang, and Deng-Feng Wang
- Subjects
0301 basic medicine ,Programmed cell death ,Cell Survival ,Apoptosis ,Myocardial Reperfusion Injury ,Ataxia Telangiectasia Mutated Proteins ,Pharmacology ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,medicine ,Animals ,Viability assay ,RNA, Small Interfering ,biology ,Caspase 3 ,Plant Extracts ,Superoxide Dismutase ,Ginkgo biloba ,Endothelial Cells ,General Medicine ,Transfection ,Hypoxia (medical) ,biology.organism_classification ,medicine.disease ,In vitro ,Rats ,Disease Models, Animal ,Oxidative Stress ,030104 developmental biology ,RNA Interference ,medicine.symptom ,Reactive Oxygen Species ,Reperfusion injury ,Signal Transduction ,Biotechnology - Abstract
Ginkgo biloba extract (EGb 761) has been widely used clinically to reduce myocardial ischemia reperfusion injury (MIRI). Microvascular endothelial cells (MVECs) may be a proper cellular model in vitro for the effect and mechanism study against MIRI. However, the protective effect of EGb 761 on MVECs resisting hypoxia/reoxygenation (H/R) injury is little reported. In this study, H/R-injured MVECs were treated with EGb 761, and then the cell viability, apoptosis, ROS production, SOD activity, caspase-3 activity, and protein level of ATM, γ-H2AX, p53, and Bax were measured. ATM siRNA was transfected to study the changes of protein in the ATM pathway. EGb 761 presented protective effect on H/R-injured MVECs, with decreasing cell death, apoptosis, and ROS, and elevated SOD activity. Next, EGb 761 could inhibit H/R-induced ATM, γ-H2AX, p53, and Bax in a dose-dependent manner. Moreover, ATM siRNA also could inhibit H/R-induced ATM, γ-H2AX, p53, and Bax. Overall, these findings verify that EGb 761 protects cardiac MVECs from H/R injury, and for the first time, illustrate the influence on the ATM pathway and apoptosis by EGb 761 via dampening ROS.
- Published
- 2017
32. The Arc Gene Confers Genetic Susceptibility to Alzheimer’s Disease in Han Chinese
- Author
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Deng-Feng Zhang, Buchang Zhang, Tao Li, Rui Bi, Guo-Dong Li, Min Xu, Yiru Fang, Chen Zhang, Yong-Gang Yao, and Li-Li Kong
- Subjects
Male ,0301 basic medicine ,China ,Neuroscience (miscellaneous) ,Nerve Tissue Proteins ,Biology ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Exon ,Asian People ,Gene Frequency ,Alzheimer Disease ,Genotype ,Genetic predisposition ,medicine ,Humans ,Dementia ,Genetic Predisposition to Disease ,Gene ,Alleles ,Genetic Association Studies ,Aged ,Genetic association ,Genetics ,Arc (protein) ,Middle Aged ,medicine.disease ,Cytoskeletal Proteins ,030104 developmental biology ,Neurology ,Case-Control Studies ,Female ,Synaptopathy - Abstract
Alzheimer's disease (AD) is the most common form of dementia. The deposition of β-amyloid (Aβ) plaques in the brain was considered one of the main neuropathological hallmarks of AD. As the loss of synapses always occurs during AD progression, AD has been gradually regarded as a "synaptopathy." The activity-regulated cytoskeleton-associated protein (Arc) was recently identified as a key factor for AD due to its active roles in synaptic plasticity, learning, memory, and Aβ generation. However, there is little evidence to support the association of the Arc gene with AD. In this study, a two-stage case-control study of 1471 Han Chinese was conducted to investigate the genetic association between the Arc gene and AD. Variant rs10097505 in the 3'UTR region was significantly associated with AD. The whole exons of the Arc gene were also screened in 99 AD patients with a high heritability (familial and/or onset age55 years old). One missense variant (c.20GA, p.T7I) was identified in two AD patients but was absent in the controls from the general populations. Both rs10097505 and c.20GA were predicted to be potentially pathogenic. Further luciferase assay, data mining, and integrative analyses revealed that the AD-risk genotype AA of rs10097505 was associated with an increased Arc mRNA expression and an elevated Aβ level. Our results indicated that the Arc gene would confer susceptibility to AD in Han Chinese, probably through changing the protein structure or affecting the Arc expression in brain tissues, which would finally contribute to the pathogenesis and development of AD.
- Published
- 2017
33. New prenylxanthones, polyketide hemiterpenoid pigments from the endophytic fungus Emericella sp. XL029 and their anti-agricultural pathogenic fungal and antibacterial activities
- Author
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Feng-Lou Liu, Deng-Feng Yang, Ting Zhao, Xue-Jiao Pang, Li-Zhen Fang, Lu-Lin Xu, Xiao-Long Yang, Hai-Li Qin, and Xia Wu
- Subjects
biology ,010405 organic chemistry ,Chemistry ,General Chemical Engineering ,Pathogenic bacteria ,General Chemistry ,biology.organism_classification ,medicine.disease_cause ,Rhizoctonia ,01 natural sciences ,Physalospora ,0104 chemical sciences ,Microbiology ,010404 medicinal & biomolecular chemistry ,Staphylococcus aureus ,Fusarium oxysporum ,medicine ,Panax notoginseng ,Antibacterial activity ,Bacteria - Abstract
Four new prenylxanthones (1–4) together with five known compounds (5–9) were isolated from the solid-substrate fermentation culture of Emericella sp. XL029 associated with the leaves of Panax notoginseng. Their structures and relative configurations were elucidated by extensive spectroscopic analysis and comparison of NMR data to those of known compounds. The anti-agricultural pathogenic fungal and antibacterial activities of all isolated compounds were evaluated against eight agricultural pathogenic fungi and nine human pathogenic bacteria. The anti-agricultural pathogenic fungal assay indicated that compounds 1, 2, 4, 8 and 9 displayed significant activity against Drechslera maydis with MIC value of 25 μg mL−1. Moreover, compound 1 also exhibited significant activity against other three fungi including Rhizoctonia cerealis, Fusarium oxysporum and Physalospora piricola, and compounds 4 and 9 against Rhizoctonia cerealis with MIC value of 25 μg mL−1. Compound 5 only demonstrated significant activity against Physalospora piricola with MIC value of 25 μg mL−1. Further antibacterial activity tests revealed that compounds 1–9 showed significant antibacterial activity against all tested Gram-positive (except for drug resistant Staphylococcus aureus) and Gram-negative bacteria with MIC values ranging from 12.5 to 50 μg mL−1. While only compounds 1, 4 and 9 displayed moderate activity against drug resistant Staphylococcus aureus with MIC value of 50 μg mL−1.
- Published
- 2017
34. The complete chloroplast genome sequence of Heracleum yungningense
- Author
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Zhen-Ying Zheng, Song-Dong Zhou, Deng-Feng Xie, Xing-Jin He, and Jun Li
- Subjects
0106 biological sciences ,0301 basic medicine ,Whole genome sequencing ,Genetics ,Heracleum yungningense ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Chloroplast ,03 medical and health sciences ,030104 developmental biology ,Molecular Biology - Abstract
Heracleum yungningense is a traditional medicinal plant widely used in China. Here, we reported the complete chloroplast genome of H. yungningense using Illumina paired-end sequencing. The whole ge...
- Published
- 2020
35. Fragmented habitat drives significant genetic divergence in the Chinese endemic plant, Urophysa henryi (Ranuculaceae)
- Author
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Deng-Feng Xie, Xian-Lin Guo, Hao-Yu Hu, Lin Zhang, and Xing-Jin He
- Subjects
0106 biological sciences ,education.field_of_study ,Genetic diversity ,Habitat fragmentation ,Ecology ,Population ,UPGMA ,Small population size ,Biology ,010603 evolutionary biology ,01 natural sciences ,Biochemistry ,Gene flow ,Spatial heterogeneity ,Genetic divergence ,education ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
Urophysa henryi (Oliv.) Ulbr., endemic to China with small populations, is known as a medicinal plant. In this study, ISSR markers were used to assess the genetic diversity and population structure throughout its entire distribution areas. Twelve primers revealed high genetic diversity at the species level (PPB = 95.6%; H = 0.3441; I = 0.5111), as well as high level of genetic differentiation (FST = 0.659, p
- Published
- 2016
36. Chloroplast genomic comparison of two sister species Allium macranthum and A. fasciculatum provides valuable insights into adaptive evolution
- Author
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Deng-Feng Xie, Jun-Pei Chen, Hao Li, Xing-Jin He, and Song-Dong Zhou
- Subjects
0106 biological sciences ,0301 basic medicine ,Plant evolution ,Phylogenetic tree ,Allium macranthum ,Biology ,biology.organism_classification ,01 natural sciences ,Biochemistry ,Genome ,Adaptation, Physiological ,Nucleotide diversity ,Allium ,Allium fasciculatum ,Evolution, Molecular ,03 medical and health sciences ,030104 developmental biology ,Evolutionary biology ,Phylogenetics ,Genetics ,Genome, Chloroplast ,Molecular Biology ,Genome size ,Phylogeny ,010606 plant biology & botany - Abstract
Allium macranthum and Allium fasciculatum are two sister species and their natural populations are separated by high mountains and deep valleys with exact opposite habitat. The chloroplast genome in angiosperms has showed useful for investigating plant evolution and systematic studies. Comparative analysis of these genomes revealed potential markers and phylogenetic analysis, and discuss the influence of positive selected sites on adaptive evolution. Here, we sequenced the complete chloroplast genomes of these two species and analyzed the repeat sequences components, nucleotide diversity, selection pressure and the phylogeny relationships with related species. A typical quadripartite structure was detected with a genome size changed from 152,148 to 152,931 bp. We identified 67 and 79 simple sequence repeats in A. macranthum and A. fasciculatum, in which the mono-nucleotide repeats A/T possess the highest percentage. Three mutational hotspots (rpl32, rps16 and matK) at the SSC and LSC regions were observed, which showed remarkably higher Pi value (> 0.03). Additionally, eight genes (rpoA, atpF, cemA, rps4, ccsA, rpoC2, rpl14 and clpP) exhibited elevated pairwise Ka/Ks ratios in alpine species. Phylogenetic analyses based on the CDS sequences and the whole complete genomes showed same topologies with high support, and A. macranthum was closely clustered with A. fasciculatum within the fourteen Amaryllidaceae species. Their coding proteins of these genes often functioned in chloroplast protein synthesis, gene transcription, energy transformation and regulation and photosynthesis. These results provide valuable insights into the alpine species adaptation and evolution.
- Published
- 2019
37. Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome
- Author
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Megan Price, Song-Dong Zhou, Yi-Qi Deng, Huan-Xi Yu, Jun-Pei Chen, Xing-Jin He, Deng-Feng Xie, Chuan Xie, and Yan Yu
- Subjects
0106 biological sciences ,0301 basic medicine ,Plant Science ,lcsh:Plant culture ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Nucleotide diversity ,Allium ,03 medical and health sciences ,Phylogenetics ,positive selection ,lcsh:SB1-1110 ,Allioideae ,Original Research ,adaptive evolution ,Phylogenetic tree ,food and beverages ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,Molecular phylogenetics ,phylogeny analyses ,chloroplast genome ,GC-content - Abstract
The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
- Published
- 2019
38. Structural and Functional Insights into PpgL, a Metal-Independent β-Propeller Gluconolactonase That Contributes to Pseudomonas aeruginosa Virulence
- Author
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Li-Hui He, Jing Yang, Jie Gao, Bo Sun, Chang-Cheng Li, Xing-Yu Mu, Qiao-Xia Zhou, Qin Huang, Jian-Hua He, Tao Li, Chang Zhao, Chuan Liu, Ninglin Zhao, Deng-Feng Dou, Rui Bao, Ying-Jie Song, Kai-Lun Wang, Yalin Shen, Hong Li, and Yi-Bo Zhu
- Subjects
0301 basic medicine ,030106 microbiology ,Immunology ,Virulence ,Biology ,medicine.disease_cause ,Microbiology ,Substrate Specificity ,Lactones ,03 medical and health sciences ,Bacterial Proteins ,medicine ,Humans ,Pseudomonas Infections ,Pseudomonas aeruginosa ,Mutagenesis ,Biofilm ,Biofilm matrix ,Periplasmic space ,Molecular Pathogenesis ,030104 developmental biology ,Infectious Diseases ,Metals ,Biofilms ,Periplasm ,Biocatalysis ,Gluconolactonase ,Parasitology ,Carboxylic Ester Hydrolases ,Function (biology) ,HeLa Cells - Abstract
Biofilm formation is a critical determinant in the pathopoiesis of Pseudomonas aeruginosa. It could significantly increase bacterial resistance to drugs and host defense. Thus, inhibition of biofilm matrix production could be regarded as a promising attempt to prevent colonization of P. aeruginosa and the subsequent infection. PpgL, a periplasmic gluconolactonase, has been reported to be involved in P. aeruginosa quorum-sensing (QS) system regulation. However, the detailed function and catalysis mechanism remain elusive. Here, the crystal structure of PpgL is described in the current study, along with biochemical analysis, revealing that PpgL is a typical β-propeller enzyme with unique metal-independent lactone hydrolysis activity. Consequently, comparative analysis of seven-bladed propeller lactone-catalyzing enzymes and mutagenesis studies identify the critical sites which contribute to the diverse catalytic and substrate recognition functions. In addition, the reduced biofilm formation and attenuated invasion phenotype resulting from deletion of ppgL confirm the importance of PpgL in P. aeruginosa pathogenesis. These results suggest that PpgL is a potential target for developing new agents against the diseases caused by P. aeruginosa.
- Published
- 2019
39. A Comprehensive Analysis of the CaMK2A Gene and Susceptibility to Alzheimer’s Disease in the Han Chinese Population
- Author
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Xinyu Fang, Jiangtao Zhang, Wei Tang, Jianliang Ni, Weihong Lu, Wenxin Tang, Chen Zhang, Tao Li, Fuyin Yang, Jun Cai, and Deng-Feng Zhang
- Subjects
0301 basic medicine ,Aging ,haplotype ,China ,Cognitive Neuroscience ,Population ,Single-nucleotide polymorphism ,Biology ,eQTL ,lcsh:RC321-571 ,03 medical and health sciences ,0302 clinical medicine ,CaMK2A ,Polymorphism (computer science) ,CAMK2A ,education ,gene ,lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry ,Original Research ,Genetics ,Temporal cortex ,education.field_of_study ,Haplotype ,Entorhinal cortex ,030104 developmental biology ,Expression quantitative trait loci ,Alzheimer’s disease ,030217 neurology & neurosurgery ,Neuroscience - Abstract
There is ample evidence suggesting that calcium/calmodulin-dependent protein kinase II alpha (CaMK2A) may play an important role in the pathophysiology of Alzheimer’s disease (AD). This genetic study aimed to investigate whether CaMK2A confers susceptibility to the development of AD in the Han Chinese population. A total of seven single nucleotide polymorphisms (SNPs) within CaMK2A were screened in two independent cohorts from southwestern China (333 AD patients and 334 controls) and eastern China (382 AD patients and 426 controls) to discern the potential association between this gene and AD. In addition, a cross-platform normalized expression resource was used to investigate whether CaMK2A is differentially expressed in the brain between individuals with AD and the controls. In addition, expression quantitative trait loci (eQTL) analysis was used to explore the differences in CaMK2A expression in the brain among different genotypes. The cross-platform normalized data showed significant differences in CaMK2A expression in the hippocampus, entorhinal cortex and temporal cortex between the AD patients and the control subjects (|log FC| > 0.1, P < 0.05); however, only the differences in the hippocampus and temporal cortex remained after the multiple comparisons correction [false discovery rate (FDR)-corrected, P < 0.05]. The frequency of the rs4958445 genotype was significantly different between the AD subjects and the controls from southwestern China (P = 0.013, P = 0.034 after FDR correction). When the two samples were combined, rs4958445 still showed a significant association with AD (P = 0.044). Haplotype analysis indicated that the T-A-C-A-T-C-C and T-G-C-A-T-C-C haplotypes in the southwestern cohort and the T-G-C-G-C-T-C haplotype in the eastern cohort, consisting of rs10051644, rs6869634, rs3797617, rs3756577, rs4958445, rs10515639 and rs6881743, showed a significant association with AD (P = 0.037, P = 0.026 and P = 0.045, respectively). Furthermore, the brain eQTL analysis revealed a significant association between the rs4958445 polymorphism and CaMK2A expression in the inferior olivary nucleus (P = 0.029). Our results suggest an important role for CaMK2A in the pathophysiology of AD in the Han Chinese population, especially the southwestern population.
- Published
- 2019
40. Identification of the primate-specific gene BTN3A2 as an additional schizophrenia risk gene in the MHC loci
- Author
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Ming Li, Xiao Xiao, Chunli Sun, Xiong-Jian Luo, Nengyin Sheng, Deng-Feng Zhang, Yong-Gang Yao, Changguo Ma, Jingzheng Li, Ping Zheng, Yong Wu, Chunhua Zeng, and Rui Bi
- Subjects
0301 basic medicine ,Primates ,Research paper ,Induced Pluripotent Stem Cells ,Quantitative Trait Loci ,Genome-wide association study ,Quantitative trait locus ,Biology ,Hippocampus ,Synaptic Transmission ,General Biochemistry, Genetics and Molecular Biology ,Workflow ,Major Histocompatibility Complex ,03 medical and health sciences ,0302 clinical medicine ,Databases, Genetic ,medicine ,Animals ,Humans ,Genetic Predisposition to Disease ,Gene ,Genetic Association Studies ,Genetic association ,Genetics ,Butyrophilins ,Gene Expression Profiling ,Brain ,Complement C4a ,Computational Biology ,Gene Expression Regulation, Developmental ,General Medicine ,Human brain ,DNA Methylation ,Mendelian Randomization Analysis ,medicine.disease ,3. Good health ,Rats ,030104 developmental biology ,medicine.anatomical_structure ,Schizophrenia ,030220 oncology & carcinogenesis ,Expression quantitative trait loci ,Glutamatergic synapse ,Genome-Wide Association Study - Abstract
Background Schizophrenia is a complex mental disorder resulting in poor life quality and high social and economic burden. Despite the fact that genome-wide association studies (GWASs) have successfully identified a number of risk loci for schizophrenia, identifying the causal genes at the risk loci and elucidating their roles in disease pathogenesis remain major challenges. Methods The summary data-based Mendelian randomization analysis (SMR) was used to integrate a large-scale GWAS of schizophrenia with brain expression quantitative trait loci (eQTL) data and brain methylation expression quantitative trait loci (meQTL) data, to identify novel risk gene(s) for schizophrenia. We then analyzed the mRNA expression and methylation statuses of the gene hit BTN3A2 during the early brain development. Electrophysiological analyses of CA1 pyramidal neurons were performed to evaluate the excitatory and inhibitory synaptic activity after overexpression of BTN3A2 in rat hippocampal slices. Cell surface binding assay was used to test the interaction of BTN3A2 and neurexins. Findings We identified BTN3A2 as a potential risk gene for schizophrenia. The mRNA expression and methylation data showed that BTN3A2 expression in human brain is highest post-natally. Further electrophysiological analyses of rat hippocampal slices showed that BTN3A2 overexpression specifically suppressed the excitatory synaptic activity onto CA1 pyramidal neurons, most likely through its interaction with the presynaptic adhesion molecule neurexins. Interpretation Increased expression of BTN3A2 might confer risk for schizophrenia by altering excitatory synaptic function. Our result constitutes a paradigm for distilling risk gene using an integrative analysis and functional characterization in the post-GWAS era. Fund This study was supported by the Strategic Priority Research Program (B) of the Chinese Academy of Sciences (XDB02020003 to Y-GY), the National Natural Science Foundation of China (31730037 to Y-GY), and the Bureau of Frontier Sciences and Education, Chinese Academy of Sciences (QYZDJ-SSW-SMC005 to Y-GY).
- Published
- 2019
41. A Phytogeographic Divide Along the 500 mm Isohyet in the Qinghai-Tibet Plateau: Insights From the Phylogeographic Evidence of Chinese Alliums (Amaryllidaceae)
- Author
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Chuan Xie, Xing-Jin He, Yan Yu, Yan Zhong, Deng-Feng Xie, Yi-Qi Deng, and Min-Jie Li
- Subjects
0106 biological sciences ,0301 basic medicine ,Range (biology) ,Qinghai-Tibet Plateau ,Plant Science ,Biology ,lcsh:Plant culture ,010603 evolutionary biology ,01 natural sciences ,Allium ,Allium fasciculatum ,03 medical and health sciences ,Vicariance ,lcsh:SB1-1110 ,Original Research ,phytogeographic divide ,Ecological niche ,Ecology ,biology.organism_classification ,Genetic divergence ,genetic breaks ,Pleistocene ,Phylogeography ,030104 developmental biology ,Genetic structure ,Subgenus - Abstract
The Qinghai-Tibet Plateau (QTP) has been biogeographically divided into the eastern monsoonal and the western continental climatic zones along the 500 mm isohyet. However, this biogeographic hypothesis has been rarely tested using a phylogeographic approach. The members of the genus Allium subgenus Cyathophora coincidentally distribute across this biogeographical divide. Intriguingly, Allium fasciculatum of subgenus Amerallium co-occurs in the distribution range of subgenus Cyathophora. To illuminate the role of this biogeographic divide on the genetic divergence, we genotyped 466 individuals of 52 populations of subgenus Cyathophora and 110 individuals of 19 populations of A. fasciculatum using three chloroplast DNA fragments, whole nrITS and nine nuclear microsatellite loci, supplemented with the present environmental space and paleo-distribution modeling. Our phylogeographical evidence recovered the concordant east-west genetic breaks both for subgenus Cyathophora and A. fasciculatum along the 500 mm isohyet. The divergence time estimations and environmental niche differentiations suggested this east-west genetic breaks could have been triggered by the climatic-induced vicariance during the early Pleistocene. Noticeably, this split within subgenus Cyathophora could have been deepened by the morphological vicariance from the eastern umbel to the western spicate, while that within A. fasciculatum could have been obscured due to the pollen flows from the east to west caused by the postglacial expansion. The genetic structures and ecological niche modelings (ENMs) recovered the distinct responses to the Quaternary climatic oscillations for species constricted to different climatic zones, further highlighting the profound effect of the climatic differences and tectonic uplifts on the genetic diversification. Overall, our findings offer strong evidence for the existence of a biogeographic divide between the eastern monsoonal and the west continental climatic zones of the QTP nearly along the 500 mm isohyet.
- Published
- 2019
42. Draft Genome Analysis Offers Insights Into the Mechanism by Which Streptomyces chartreusis WZS021 Increases Drought Tolerance in Sugarcane
- Author
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Zhen Wang, Manoj Kumar Solanki, Zhuo-Xin Yu, Li-Tao Yang, Qian-Li An, Deng-Feng Dong, and Yang-Rui Li
- Subjects
plant growth promotion ,Microbiology (medical) ,Siderophore ,Drought tolerance ,lcsh:QR1-502 ,Biomass ,Microbiology ,Streptomyces ,Endophyte ,lcsh:Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,sugarcane ,Proline ,genome ,Original Research ,030304 developmental biology ,Abiotic component ,0303 health sciences ,biology ,030306 microbiology ,drought stress ,fungi ,food and beverages ,biology.organism_classification ,Horticulture ,chemistry ,Chlorophyll - Abstract
Drought directly affects sugarcane production. Plant growth-promoting bacteria have gained attention as growth promoters of plants under abiotic stresses. The present study focused on genome assessment of the plant-beneficial endophyte Streptomyces chartreusis WZS021 and its vital role in sugarcane plants under drought stress. Based on in vitro plant growth-promoting trait analyses, WZS021 had multiple abilities, including tolerance to drought and production of 1-aminocyclopropane-1-carboxylic deaminase, siderophores, and indole acetic acid. We confirmed root colonization of sugarcane transplants by WZS021 by a sterile sand assay and scanning electron microscopy. Plants inoculated with strain WZS021 had a positive influence on the root parameters such as length and biomass when compared to the control plants. A comparative study of the responses of two sugarcane varieties (ROC22 and B8) to different levels of drought stress in the presence or absence of WZS021 was conducted by assessing the plant chemistry. The expression of antioxidants in sugarcane leaves varied with water stress level. WZS021 inoculation improved the contents of chlorophyll, proline, and phytohormones, revealing some potential for the mechanisms by which this strain improves drought tolerance in sugarcane plants. We identified several genes that might be involved in the plant growth- and drought tolerance-promoting effects of this strain.
- Published
- 2019
43. Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers
- Author
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Dan-Mei Su, Xian-Lin Guo, Xing-Jin He, Juan Li, Hai-Ying Liu, Fu-Min Xie, Deng-Feng Xie, and Song-Dong Zhou
- Subjects
0106 biological sciences ,0301 basic medicine ,Nuclear gene ,Inverted repeat ,lcsh:Medicine ,010603 evolutionary biology ,01 natural sciences ,Genome ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Complete sequence ,Phylogenetics ,Plastid ,Lilium lankongense ,Phylogeny ,Lilium ,biology ,Phylogenetic tree ,General Neuroscience ,lcsh:R ,General Medicine ,biology.organism_classification ,Plastid genome ,030104 developmental biology ,Evolutionary biology ,Lilium-specific primers ,General Agricultural and Biological Sciences - Abstract
Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei, L. stewartianum, L. matangense, L. lophophorum, and L. nanum. However, molecular markers still lack sufficient signals for population-level research of the genus Lilium. We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions (trnC-petN and rpl32-trnL) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium.
- Published
- 2021
44. Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing
- Author
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Jun Wen, Deng-Feng Xie, Xing-Jin He, Song-Dong Zhou, Jiao Huang, Jun-Pei Chen, Yan Yu, and Juan Li
- Subjects
0106 biological sciences ,0301 basic medicine ,China ,Acclimatization ,Flowers ,Biology ,Genes, Plant ,010603 evolutionary biology ,01 natural sciences ,Allium ,Coalescent theory ,Transcriptome ,03 medical and health sciences ,Phylogenetics ,Genetics ,Endemism ,Molecular Biology ,Gene ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Gene Expression Profiling ,food and beverages ,Amaryllidaceae ,biology.organism_classification ,Plant Leaves ,030104 developmental biology ,Evolutionary biology ,Adaptation - Abstract
Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.
- Published
- 2020
45. Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship
- Author
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Deng-Feng Xie, Xing-Jin He, Xian-Lin Guo, Jun Li, Song-Dong Zhou, and Zhen-Ying Zheng
- Subjects
0106 biological sciences ,0301 basic medicine ,Bupleurum ,comparative analysis ,Plant Science ,phylogeny ,010603 evolutionary biology ,01 natural sciences ,DNA barcoding ,03 medical and health sciences ,Monophyly ,Phylogenetics ,plastid genome ,Clade ,Ecology, Evolution, Behavior and Systematics ,Ecology ,biology ,Phylogenetic tree ,Botany ,biology.organism_classification ,Chamaesium ,030104 developmental biology ,Evolutionary biology ,QK1-989 ,Bupleurum chinense ,Apiaceae - Abstract
Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae.
- Published
- 2020
46. Emericellins A and B: Two sesquiterpenoids with an unprecedented tricyclo[4,4,2,1]hendecane scaffold from the liquid cultures of endophytic fungus Emericella sp. XL 029
- Author
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Xue-Jiao Pang, Hai-Yan Fu, Xia Wu, Deng-Feng Yang, Peng-Jie Xian, Xiao-Long Yang, and Shuai-Bing Zhang
- Subjects
China ,Bacillus cereus ,Panax notoginseng ,Botryosphaeria dothidea ,Bacillus subtilis ,Microbial Sensitivity Tests ,medicine.disease_cause ,01 natural sciences ,Microbiology ,Anti-Infective Agents ,Emericella sp ,Drug Discovery ,medicine ,Endophytes ,Verticillium dahliae ,Escherichia coli ,Pharmacology ,Emericella ,biology ,Molecular Structure ,010405 organic chemistry ,Chemistry ,fungi ,General Medicine ,Endophytic fungus ,biology.organism_classification ,0104 chemical sciences ,Plant Leaves ,010404 medicinal & biomolecular chemistry ,Sesquiterpenes - Abstract
Two novel sesquiterpenoids with an unprecedented tricyclo[4,4,2,1]hendecane scaffold, namely emericellins A (1) and B (2) representing a new skeleton, were isolated from the liquid cultures of an endophytic fungus Emericella sp. XL 029 associated with the leaves of Panax notoginseng. Their structures and relative configurations were characterized by extensive spectroscopic methods. Compounds 1–2 displayed moderate activities against three fungal strains (Verticillium dahliae Kleb, Helminthosporium maydis, and Botryosphaeria dothidea) and three bacterial strains (Bacillus subtilis, Bacillus cereus and Escherichia coli) with MIC values of 25–50 μg/mL.
- Published
- 2018
47. Molecular phylogenetics and historical biogeography of the tribe Lilieae (Liliaceae): bi-directional dispersal between biodiversity hotspots in Eurasia
- Author
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Song-Dong Zhou, Xing-Jin He, Deng-Feng Xie, Yan Yu, Yan-Mei Liu, Jiao Huang, Li-Qin Yang, and Juan Li
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0106 biological sciences ,0301 basic medicine ,Paraphyly ,Plant Dispersal ,Range (biology) ,Lineage (evolution) ,Biogeography ,DNA, Chloroplast ,Biodiversity ,Original Articles ,Plant Science ,Biology ,Biological Evolution ,010603 evolutionary biology ,01 natural sciences ,Phylogeography ,03 medical and health sciences ,Monophyly ,030104 developmental biology ,Taxon ,Evolutionary biology ,Molecular phylogenetics ,Liliaceae ,Biological dispersal ,Phylogeny - Abstract
BACKGROUND AND AIMS: The role played by the Qinghai–Tibet Plateau (QTP) in the organismal diversification and biogeography of plants in the Northern Hemisphere has attracted much attention from evolutionary biologists. Here we use tribe Lilieae (Liliaceae), including primarily temperate and alpine lineages with disjunct distributions in the North Temperate Zone, as a case study to shed light upon these processes. METHODS: Using 191 taxa (five outgroup taxa) comprising more than 60 % of extant Lilieae species across the entire geographical range, we analyse phylogenetic relationships based on three plastid markers (matK, rbcL, rpl16) and nuclear ITS. Divergence time estimation and ancestral range reconstruction were further inferred. KEY RESULTS: The results support a monophyletic Lilieae divided into four clades. Lilium is nested within Fritillaria, which is paraphyletic and partitioned into two clades, New World and Old World, in the chloroplast DNA (cpDNA) analysis. Incongruences between the ITS and cpDNA trees may be explained by divergent ITS paralogues and hybridization. Lilieae originated around 40–49 (28–67) Mya and probably diversified in the QTP region with four major clades that were established during the Oligocene and the Early Miocene. Uplift of the QTP and climatic changes probably drove early diversification of Lilieae in the QTP region. A rapid radiation occurred during the Late Miocene and the Pleistocene, coinciding temporally with recent orogenic process in the QTP region and climatic oscillations. Several lineages dispersed out of the QTP. CONCLUSIONS: Lineage persistence and explosive radiation were important processes for establishing high species diversity of Lilieae in the QTP region. Both long-distance dispersal and migration across Beringia probably contributed to the modern distribution range of Lilieae. Our study shows that biotic interchanges between the QTP region and Irano-Turanian region and the Mediterranean Basin were bi-directional, suggesting the latter was a secondary centre of diversity.
- Published
- 2018
48. Sequencing and analyses on chloroplast genomes of Tetrataenium candicans and two allies give new insights on structural variants, DNA barcoding and phylogeny in Apiaceae subfamily Apioideae
- Author
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Yan Yu, Chang Peng, Lu Kang, Qun-Ying Xiao, Xing-Jin He, and Deng-Feng Xie
- Subjects
DNA barcodes ,Population ,lcsh:Medicine ,Plant Science ,DNA barcoding ,Genome ,General Biochemistry, Genetics and Molecular Biology ,DNA sequencing ,Monophyly ,Phylogenetics ,Chloroplast genome ,education ,Phylogeny ,education.field_of_study ,Population Biology ,biology ,General Neuroscience ,lcsh:R ,Biodiversity ,Genomics ,General Medicine ,biology.organism_classification ,Evolutionary Studies ,Tetrataenium candicans ,Chloroplast DNA ,Evolutionary biology ,Tordyliinae ,Selineae ,Structural variants ,General Agricultural and Biological Sciences - Abstract
Background Tetrataenium candicans is a traditional Chinese folk herbal medicine used in the treatment of asthma and rheumatic arthritis. Alongside several Tordyliinae species with fleshy roots, it is also regarded as a substitute for a Chinese material medicine called ‘Danggui’. However, a lack of sufficient sampling and genomic information has impeded species identification and the protection of wild resources. Methods The complete chloroplast genomes of T. candicans from two populations, Tetrataenium yunnanense and Semenovia transilliensis, were assembled from two pipelines using data generated from next generation sequencing (NGS). Pseudogenes, inverted repeats (IRs) and hyper-variable regions were located by Geneious 11.1.5. Repeat motifs were searched using MISA and REPuter. DNA polymorphism and segment screening were processed by DNAsp5, and PCR product was sequenced with Sanger’s sequencing method. Phylogeny was inferred by MEGA 7.0 and PhyML 3.0. Results The complete chloroplast genomes of T. candicans from two populations, T. yunnanense and S. transilliensis, were 142,261 bp, 141,985 bp, 142,714 bp and 142,145 bp in length, respectively, indicating conservative genome structures and gene categories. We observed duplications of trnH and psbA caused by exceptional contractions and expansions of the IR regions when comparing the four chloroplast genomes with previously published data. Analyses on DNA polymorphism located 29 candidate cp DNA barcodes for the authentication of ‘Danggui’ counterfeits. Meanwhile, 34 hyper-variable markers were also located by the five Tordyliinae chloroplast genomes, and 11 of them were screened for population genetics of T. candicans based on plastome information from two individuals. The screening results indicated that populations of T.candicans may have expanded. Phylogeny inference on Apiaceae species by CDS sequences showed most lineages were well clustered, but the five Tordyliinae species failed to recover as a monophyletic group, and the phylogenetic relationship between tribe Coriandreae, tribe Selineae, subtribe Tordyliinae and Sinodielsia clade remains unclear. Discussion The four chloroplast genomes offer valuable information for further research on species identification, cp genome structure, population demography and phylogeny in Apiaceae subfamily Apioideae.
- Published
- 2019
49. Strong static magnetic field delayed the early development of zebrafish
- Author
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Bing Hu, Shuchao Ge, Yuan Cai, Deng-feng Huang, Hongyuan Jiang, Jun Fang, and Jingchen Li
- Subjects
Embryo, Nonmammalian ,Zygote ,Immunology ,Biology ,General Biochemistry, Genetics and Molecular Biology ,microtubules ,03 medical and health sciences ,0302 clinical medicine ,Animals ,lcsh:QH301-705.5 ,Zebrafish ,030304 developmental biology ,mitosis ,0303 health sciences ,strong static magnetic field ,Research ,General Neuroscience ,spindle ,zebrafish ,Magnetostatics ,biology.organism_classification ,early development ,Cell biology ,Magnetic Fields ,lcsh:Biology (General) ,Magnetobiology ,030217 neurology & neurosurgery ,Research Article - Abstract
One of the major topics in magnetobiology is the biological effects of strong static magnetic field (SMF) on living organisms. However, there has been a paucity of the comprehensive study of the long-term effects of strong SMF on an animal's development. Here, we explored this question with zebrafish, an excellent model organism for developmental study. In our research, zebrafish eggs, just after fertilization, were exposed to a 9.0 T SMF for 24 h, the critical period of post-fertilization development from cleavage to segmentation. The effects of strong SMF exposure on the following developmental progress of zebrafish were studied until 6 days post-fertilization (dpf). Results showed that 9.0 T SMF exposure did not influence the survival or the general developmental scenario of zebrafish embryos. However, it slowed down the developmental pace of the whole animal, and the late developers would catch up with their control peers after the SMF was removed. We proposed a mechanical model and deduced that the development delaying effect was caused by the interference of SMF in microtubule and spindle positioning during mitosis, especially in early cleavages. Our research data provide insights into how strong SMF influences the developing organisms through basic physical interactions with intracellular macromolecules.
- Published
- 2019
50. Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution
- Author
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Deng-Feng Xie, Yi-Qi Deng, Song-Dong Zhou, Hai-Ying Liu, Yan Yu, Xing-Jin He, and Juan Li
- Subjects
0301 basic medicine ,Inverted repeat ,Urophysa ,Biology ,phylogeny ,Genome ,Catalysis ,Nucleotide diversity ,positive selection analysis ,Inorganic Chemistry ,lcsh:Chemistry ,03 medical and health sciences ,Phylogenetics ,Coding region ,Semiaquilegia adoxoides ,cp genome ,Physical and Theoretical Chemistry ,Molecular Biology ,Genome size ,lcsh:QH301-705.5 ,Spectroscopy ,Illumina dye sequencing ,Phylogenetic tree ,repeat analysis ,Organic Chemistry ,General Medicine ,Computer Science Applications ,030104 developmental biology ,SSRs ,lcsh:Biology (General) ,lcsh:QD1-999 ,Evolutionary biology - Abstract
Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate the intra- and interspecies variations, and infer the phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure was detected, with a genome size from 158,473 to 158,512 bp, consisting of a pair of inverted repeats separated by a small single-copy region and a large single-copy region. We analyzed the nucleotide diversity and repeated sequences components and conducted a positive selection analysis by the codon-based substitution on single-copy coding sequence (CDS). Seven regions were found to possess relatively high nucleotide diversity, and numerous variable repeats and simple sequence repeats (SSR) markers were detected. Six single-copy genes (atpA, rpl20, psaA, atpB, ndhI, and rbcL) resulted to have high posterior probabilities of codon sites in the positive selection analysis, which means that the six genes may be under a great selection pressure. The visualization results of the six genes showed that the amino acid properties across each column of all species are variable in different genera. All these regions with high nucleotide diversity, abundant repeats, and under positive selection will provide potential plastid markers for further taxonomic, phylogenetic, and population genetics studies in Urophysa and its relatives. Phylogenetic analyses based on the 79 single-copy genes, the whole complete genome sequences, and all CDS sequences showed same topologies with high support, and U. rockii was closely clustered with U. henryi within the Urophysa genus, with S. adoxoides as their closest relative. Therefore, the complete cp genomes in Urophysa species provide interesting insights and valuable information that can be used to identify related species and reconstruct their phylogeny.
- Published
- 2018
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