Differential Impacts on Bacterial Composition and Abundance in Rhizosphere Compartments between Al-Tolerant and Al-Sensitive Soybean Genotypes in Acidic Soil

Wen Zhong-Ling,Yang Min-Kai,Fazal Aliya,Liao Yong-Hui,Cheng Lin-Run,Hua Xiao-Mei,Hu Dong-Qing,Shi Ji-Sen,Yang Rong-Wu,Lu Gui-Hua,Qi Jin-Liang,Zhi Hong,Qian Qiu-Ping,Yang Yong-Hua 한국미생물·생명공학회 2020 Journal of microbiology and biotechnology Vol.30 No.8

In this study, two soybean genotypes, i.e., aluminum-tolerant Baxi 10 (BX10) and aluminumsensitive Bendi 2 (BD2), were used as plant materials and acidic red soil was used as growth medium. The soil layers from the inside to the outside of the root are: rhizospheric soil after washing (WRH), rhizospheric soil after brushing (BRH) and rhizospheric soil at two sides (SRH), respectively. The rhizosphere bacterial communities were analyzed by high-throughput sequencing of V4 hypervariable regions of 16S rRNA gene amplicons via Illumina MiSeq. The results of alpha diversity analysis showed that the BRH and SRH of BX10 were significantly lower in community richness than that of BD2, while the WRH exhibited no significant difference between BX10 and BD2. Among the three sampling compartments of the same soybean genotype, WRH had the lowest community richness and diversity while showing the highest coverage. Beta diversity analysis results displayed no significant difference for any compartment between the two genotypes, or among the three different sampling compartments for any same soybean genotype. However, the relative abundance of major bacterial taxa, specifically nitrogen-fixing and/or aluminum-tolerant bacteria, was significantly different in the compartments of the BRH and/or SRH at phylum and genus levels, indicating genotype-dependent variations in rhizosphere bacterial communities. Strikingly, as compared with BRH and SRH, the WRH within the same genotype (BX10 or BD2) always had an enrichment effect on rhizosphere bacteria associated with nitrogen fixation

The effect of iron dextran on the transcriptome of pig hippocampus

Ling Gan,Binyu Yang,Hongyuan Mei 한국유전학회 2017 Genes & Genomics Vol.39 No.1

The chain of events resulting from oxidative stress is still barely understood. The hippocampus is particularly vulnerable to oxidative stress. With the emergence of high-throughput sequencing, many different biological components can be discovered simultaneously. Using RNA-seq technology, we conducted a whole-transcriptome analysis of the hippocampi of piglets exposed to iron dextran (FeDex), a potent inducer of oxidation stress. The total hippocampal RNA from the piglets was sequenced, and 11.5 Gb of sequencing data were obtained. Regulatory molecules involved in oxidative stress were determined through the identification of 362 differentially expressed genes (DEGs). The functional analysis revealed that these DEGs were primarily involved in the defense response and responses to external stimuli. Furthermore, 76 neuropeptide gene transcripts and 60 neuropeptide receptor gene transcripts were identified in the hippocampus. Of these transcripts, the mRNA levels of six neuropeptide genes were significantly changed. Overall, this study describes the first use of RNA-seq to elucidate the transcriptomic changes in the piglet hippocampus caused directly by the injection of iron dextran, which enabled the characterization of the transcriptional response triggered by oxidative stress.

Cytological, genetic, and proteomic analysis of a sesame (Sesamum indicum L.) mutant Siyl‑1 with yellow–green leaf color

Tong‑Mei Gao,Shuang‑Ling Wei,Jing Chen,Yin Wu,Feng Li,Li‑Bin Wei,Chun Li,Yan‑Juan Zeng,Yuan Tian,Dong‑Yong Wang,Hai‑Yang Zhang 한국유전학회 2020 Genes & Genomics Vol.42 No.1

Background Both photosynthetic pigments and chloroplasts in plant leaf cells play an important role in deciding on the photosynthetic capacity and efficiency in plants. Systematical investigating the regulatory mechanism of chloroplast development and chlorophyll (Chl) content variation is necessary for clarifying the photosynthesis mechanism for crops. Objective This study aims to explore the critical regulatory mechanism of leaf color mutation in a yellow–green leaf sesame mutant Siyl-1. Methods We performed the genetic analysis of the yellow-green leaf color mutation using the F2 population of the mutant Siyl-1. We compared the morphological structure of the chloroplasts, chlorophyll content of the three genotypes of the mutant F2 progeny. We performed the two-dimensional gel electrophoresis (2-DE) and compared the protein expression variation between the mutant progeny and the wild type. Results Genetic analysis indicated that there were 3 phenotypes of the F2 population of the mutant Siyl-1, i.e., YY type with light-yellow leaf color (lethal); Yy type with yellow-green leaf color, and yy type with normal green leaf color. The yellowgreen mutation was controlled by an incompletely dominant nuclear gene, Siyl-1. Compared with the wild genotype, the chloroplast number and the morphological structure in YY and Yy mutant lines varied evidently. The chlorophyll content also significantly decreased (P < 0.05). The 2-DE comparison showed that there were 98 differentially expressed proteins (DEPs) among YY, Yy, and yy lines. All the 98 DEPs were classified into 5 functional groups. Of which 82.7% DEPs proteins belonged to the photosynthesis and energy metabolism group. Conclusion The results revealed the genetic character of yellow-green leaf color mutant Siyl-1. 98 DEPs were found in YY and Yy mutant compared with the wild genotype. The regulation pathway related with the yellow leaf trait mutation in sesame was analyzed for the first time. The findings supplied the basic theoretical and gene basis for leaf color and chloroplast development mechanism in sesame.

Comparative Phylogenetic Relationships and Genetic Structure of the Caterpillar Fungus Ophiocordyceps sinensis and Its Host Insects Inferred from Multiple Gene Sequences

Qing-Mei Quan,Qing-Xia Wang,Xue-Li Zhou,Shan Li,Xiao-Ling Yang,Yun-Guo Zhu,Zhou Cheng 한국미생물학회 2014 The journal of microbiology Vol.52 No.2

Ophiocordyceps sinensis (Ascomycota: Ophiocordycipitaceae)is a native fungal parasite of Hepialidae caterpillars and oneof the most economically important medicinal caterpillarfungi in China. However, little is known about the phylogeneticand evolutionary relationships between O. sinensis andits host insects. In this study, nuclear ITS and β-tubulin sequencesfrom O. sinensis and mitochondrial COI, COII, andCytb sequences from its hosts were analyzed across 33 populationssampled from five regions in China. Phylogenetically,both O. sinensis and its hosts were divided into three geographicallycorrelated clades, and their phylogenies were congruent. Analysis of molecular variance and calculated coefficientsof genetic differentiation revealed significant geneticdivergence among the clades within both O. sinensis (FST=0.878, NST=0.842) and its hosts (FST=0.861, NST=0.816). Estimatedgene flow was very low for O. sinensis (Nm=0.04) andthe host insects (Nm=0.04) among these three clades. Manteltests demonstrated a significant correlation (P<0.01) betweenthe genetic distances for O. sinensis and its hosts, as well as asignificant association (P<0.05) between geographic and geneticdistances in both. The similar phylogenetic relationships,geographic distributions, and genetic structure and differentiationbetween O. sinensis and its hosts imply that they have coevolved.

Expression of microRNAs associated with oxidative stress in the hippocampus of piglets

Binyu Yang,Hongyuan Mei,Fuyuan Zuo,Ling Gan 한국유전학회 2017 Genes & Genomics Vol.39 No.7

Oxidative stress is associated with human diseases and the developmental retardation of animals. The hippocampus is particularly vulnerable to oxidative stress. MicroRNAs (miRNAs), expressed largely in the mammalian brain, are emerging as robust players and have been implicated in many cellular processes. The present study investigated the sub-tissue specificity of miRNA expression in the dorsal hippocampus (DH) and ventral hippocampus (VH) and evaluated the effects of oxidative stress induced by iron dextran (FeDex) treatment on miRNA expression in the DH and VH of pigs using RNA-sequencing technology and bioinformatics, respectively. The results demonstrated that the injection of FeDex significantly increased the levels of several markers of oxidative stress in serum of Rongchang piglets, which indicated that oxidative stress was successfully induced. Sub-tissue specificity was displayed with 54 differentially expressed miRNAs between the VH and DH. The induced oxidative stress emphasized 59 and 46 differentially expressed miRNAs in the DH and VH, respectively. GO and KEGG pathway analyses revealed that the predicted targets of these differentially expressed miRNAs were involved in the pathways that regulate the expression of genes associated with nervous system development, immune response and oxidative stress, which not only revealed the ability of miRNAs to influence complex gene networks in the DH and VH but also further corroborated the successful induction of oxidative stress. Collectively, the results of this study provide a valuable basis for future studies aimed at contributions of miRNAs induced by oxidative stress in growth retardation and neurodegenerative diseases of animals and human.

Inhibitory effect of raspberry ketone on α-glucosidase: Docking simulation integrating inhibition kinetics

Xiong, Shang-Ling,Yue, Li-Mei,Lim, Gyu Tae,Yang, Jun-Mo,Lee, Jinhyuk,Park, Yong-Doo Elsevier 2018 INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES Vol.113 No.-

<P><B>Abstract</B></P> <P>Inhibition of α-glucosidase is directly associated with treatment of type 2 diabetes. In this regard, we conducted enzyme kinetics integrated with computational docking simulation to assess the inhibitory effect of raspberry ketone (RK) on α-glucosidase. RK bound to the active site of α-glucosidase and interacted with several key residues such as ASP68, TYR71, HIS111, PHE157, PHE158, PHE177, GLN181, ASP214, THR215, ASP349, ASP408, and ARG439, as detected by protein-ligand docking simulation. Subsequently, we confirmed the action of RK on α-glucosidase as the non-competitive type of inhibition in a reversible and rapidly binding manner. The relevant kinetic parameters were <I>IC</I> <SUB>50</SUB> =6.17±0.46mM and <I>K</I> <SUB> <I>i</I> </SUB> =7.939±0.211mM. Regarding the structure-activity relationship, the higher concentration of RK induced slight modulation of the shape of the active site as monitored by hydrophobic exposure. The tertiary conformational change was linked to RK inhibition, and mostly involved regional changes of the active site. Our study provides insight into the functional role of RK due to its structural property of a hydroxyphenyl ring that interacts with the active site of α-glucosidase. We suggest that similar hydroxyphenyl ring compounds targeting the key residues of the active site might be potential α-glucosidase inhibitors.</P>

Tensile Test and Numerical Simulation Investigations on the Mechanical Properties of a New Type of Slightly Curved Arc HRB400 Steel Bars in Mass Concrete

Li Gao,Mei-Ling Zhuang,Fangzhi Zhu,Chuanzhi Sun,Jun Yang 한국콘크리트학회 2023 International Journal of Concrete Structures and M Vol.17 No.5

The temperature stress in mass concrete structure is relatively high during construction, which usually leads to temperature cracks. To solve this problem, concrete blocks are usually placed by setting wide slots. Connecting the truncated steel bars at the position of the wide slots by welding or extruding sleeves has many disadvantages. To solve the problem of temperature-induced stress loss, a new type of slightly curved arc HRB400 (SCAHRB400) steel bars was proposed without cutting off the steel bars in this article. Tensile tests and numerical simulations were performed for five types of SCAHRB400 steel bars considering geometric and material nonlinearity. Based on the test results and numerical simulation results, the equivalent stress–strain relationships of SCAHRB400 steel bars were established, and the emergence of the plastic zone of SCAHRB400 steel bars in the tensile process were observed, the tensile properties of SCAHRB400 steel bars were analyzed and discussed. The test results indicate that SCAHRB400 steel bars are prone to local yielding near the crown of large arches and at the connection of horizontal and arc sections. The numerical simulation equivalent stress–strain curves have good regularity. The equivalent stress–strain curves of slightly curved arc HRB400 and HRB335 steel bars have the similar changing law. When the stress is small, the tensile stiffness and compressive axial stiffness of slightly curved arc HRB400 and HRB335 steel bars are similar; when the stress is large, the axial stiffness of SCAHRB400 steel bars is greater than that of slight curved arc HRB335 steel bars. Through test and numerical simulation studies, the theoretical basis can be established for the engineering application of new slightly curved arc steel bars in mass concrete.

Cloning, Expression, and Characterization of Endoglucanase Gene egIV from Trichoderma viride AS 3.3711

( Huang Xiao Mei ),( Jin Xia Fan ),( Qian Yang ),( Xiu Ling Chen ),( Zhi Hua Liu ),( Yun Wang ),( Da Qing Wang ) 한국미생물 · 생명공학회 2012 Journal of microbiology and biotechnology Vol.22 No.3

Endoglucanase gene egIV was cloned from Trichoderma viride AS 3.3711, an important cellulose-producing fungus, by using an RT-PCR protocol. The egIV cDNA is 1,297 bp in length and contains a 1,035 bp open reading frame encoding a 344 amino acid protein with an estimated molecular mass of 35.5 kDa and isoelectronic point (pI) of 5.29. The expression of gene egIV in T. viride AS 3.3711 could be induced by sucrose, corn straw, carboxymethylcellulose (CMC), or microcrystalline cellulose, but especially by CMC. The transcripts of egIV were regulated under these substrates, but the expression level of the egIV gene could be inhibited by glucose and fructose. Three recombinant vectors, pYES2-xegIV, pYES2Mα-egIV, and pYES2Mα-xegIV, were constructed to express the egIV gene in Saccharomyces cerevisiae H158. The CMCase activity of yeast transformants IpYES2Mα-xegIV was higher than that of transformant IpYES2-xegIV or IpYES2Mα-egIV, with the highest activity of 0.13 U/ml at induction for 48 h, illustrating that the modified egIV gene could enhance CMCase activity and that MFα signal peptide from S. cerevisiae could regulate exogenous gene expression more effectively in S. cerevisiae. The recombinant EGIV enzyme was stable at pH 3.5 to 7.5 and temperature of 35oC to 65oC. The optimal reaction condition for EGIV enzyme activity was at the temperature of 55oC, pH of 5.0, 0.75 mM Ba2+, and using CMC as substrate. Under these conditions, the highest activity of EGIV enzyme in transformant IpYES2Mα-xegIV was 0.18 U/ml. These properties would provide technical parameters for utilizing cellulose in industrial bioethanol production.

AZD1480 Can Inhibit the Biological Behavior of Ovarian Cancer SKOV3 Cells in vitro

Sun, Zhao-Ling,Tang, Ya-Juan,Wu, Wei-Guang,Xing, Jun,He, Yan-Fang,Xin, De-Mei,Yu, Yan-Li,Yang, Yang,Han, Ping Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.8

Objective: To study the mechanism of effects of AZD1480 on the SKOV3 ovarian cancer cell line. Methods: The MTT method was used to assess cellular proliferation, flow cytometry for cellular apoptosis, the scratch test to determine migration, transwell chamber assays to detect cellular invasion, plate clone experiments to detect the clone forming ability and Western blotting to determine p-STAT3 protein levels. Results: The proliferation rate, migration ability, invasiveness and the clone forming ability of SKOV3 cells were reduced after treatment with AZD1480, while apoptosis rate and chemotherapeutic susceptibility were increased. After treatment with AZD1480 plus cisplatin, the apoptosis rate increased significantly while the expression level of p-STAT3 protein was decreased. Conclusion: AZD1480 can inhibit the proliferation, invasion, metastasis and clone formation of SKOV3 cells, induce cellulsar apoptosis, increase the chemotherapeutic sensitivity and reduce the expression level of p-STAT3 protein.

Covalent Immobilization of Penicillin G Acylase onto Fe₃O₄@Chitosan Magnetic Nanoparticles

( Xiao Min Ling ),( Xiang Yu Wang ),( Ping Ma ),( Yi Yang ),( Jie Mei Qin ),( Xue Jun Zhang ),( Ye Wang Zhang ) 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.5

Penicillin G acylase (PGA) was immobilized on magnetic Fe₃O₄@chitosan nanoparticles through the Schiff base reaction. The immobilization conditions were optimized as follows: enzyme/support 8.8 mg/g, pH 6.0, time 40 min, and temperature 25℃. Under these conditions, a high immobilization efficiency of 75% and a protein loading of 6.2 mg/g-support were obtained. Broader working pH and higher thermostability were achieved by the immobilization. In addition, the immobilized PGA retained 75% initial activity after ten cycles. Kinetic parameters Vmax and Km of the free and immobilized PGAs were determined as 0.113 mmol/min/mg-protein and 0.059 mmol/min/mg-protein, and 0.68 mM and 1.19 mM, respectively. Synthesis of amoxicillin with the immobilized PGA was carried out in 40% ethylene glycol at 25℃ and a conversion of 72% was obtained. These results showed that the immobilization of PGA onto magnetic chitosan nanoparticles is an efficient and simple way for preparation of stable PGA.