Identification of Long Non-Coding RNAs and Their Target Genes from Mycelium and Primordium in Model Mushroom Schizophyllum commune

Tuheng Wu,Jian Chen,Chunwei Jiao,Huiping Hu,Qingping Wu,Yizhen Xie 한국균학회 2022 Mycobiology Vol.50 No.5

Schizophyllum commune has emerged as the most promising model mushroom to study developmental stages (mycelium, primordium), which are two primary processes of fruit body development. Long non-coding RNA (lncRNA) has been proved to participate in fruit development and sex differentiation in fungi. However, potential lncRNAs have not been identified in S. commune from mycelium to primordium developmental stages. In this study, lncRNA-seq was performed in S. commune and 61.56 Gb clean data were generated from mycelium and primordium developmental stages. Furthermore, 191 lncRNAs had been obtained and a total of 49 lncRNAs were classified as differently expressed lncRNAs. Additionally, 26 up-regulated differently expressed lncRNAs and 23 down-regulated between mycelium and primordia libraries were detected. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed lncRNAs target genes from the MAPK pathway, phosphatidylinositol signal, ubiquitin-mediated proteolysis, autophagy, and cell cycle. This study provides a new resource for further research on the relationship between lncRNA and two developmental stages (mycelium, primordium) in S. commune.

Vibrio parahaemolyticus cqsA controls production of quorum sensing signal molecule 3-hydroxyundecan-4-one and regulates colony morphology

Kui Wu,Yangyun Zheng,Qingping Wu,Haiying Chen,Songzhe Fu,Biao Kan,Yongyan Long,Xiansheng Ni,Junling Tu 한국미생물학회 2019 The journal of microbiology Vol.57 No.12

In order to adapt to different environments, Vibrio parahaemolyticus employed a complicated quorum sensing system to orchestrate gene expression and diverse colony morphology patterns. In this study, the function of the putative quorum sensing signal synthase gene cqsA (VPA0711 in V. parahaemolyticus strain RIMD2210633 genome) was investigated. The cloning and expression of V. parahaemolyticus cqsA in Escherichia coli system induced the production of a new quorum sensing signal that was found in its culture supernatant. The signal was purified by high performance liquid chromatography methods and determined to be 3-hydroxyundecan- 4-one by indirect and direct mass spectra assays. The deletion of cqsA in RIMD2210633 changed V. parahaemolyticus colony morphology from the classical ‘fried-egg’ shape (thick and opaque in the center, while thin and translucent in the edge) of the wild-type colony to a ‘pancake’ shape (no significant difference between the centre and the edge) of the cqsAdeleted colony. This morphological change could be restored by complementary experiment with cqsA gene or the signal extract. In addition, the expression of opaR, a well-known quorum sensing regulatory gene, could be up-regulated by cqsA deletion. Our results suggested that V. parahaemolyticus used cqsA to produce 3-hydroxyundecan-4-one signal and thereby regulated colony morphology and other quorum sensing-associated behaviors.

Co spin state and magnetic structure in GdBaCo2O5þx and Fe doped compounds: A first principles study

Qingping Zhang,Xiusheng Wu,Eerjun Kan 한국물리학회 2016 Current Applied Physics Vol.16 No.9

GdBaCo2O5.5 exhibits impressive application potentials on giant magnetic resistance materials and solid oxide fuel cell cathodes, owing to its unique electrical and magnetic properties. In this article, stable magnetic-order structures of Co in GdBaCo2O5.5, Fe doped compounds, and GdBaCo2O5.25 with additional oxygen vacancy deficients, are investigated based on first principles calculations. Comparisons with reported experiments are also presented. It turns out that G type antiferromagnetic ordering is the most stable under ground state, and Co is high-spin state, which matches the observations of neutron diffraction and XAS spectrum. Calculated results show that the stability of ferromagnetic phase under low temperature will be enhanced by the introduction of Fe dopant, which is supported by the reported experiment. Moreover, additional oxygen vacancies caused by the valence alternation of Co ions are discussed. The magnetic moments of several Co cations closed to the additional vacancy are reduced. Besides, oxygen ions could be divided into 3 layers based on their stabilities. Oxygen vacancy formation energies within two layers are much lower, which facilitate the oxygen ion transfer along these layers. This result also fits the conclusion of reported molecular dynamic simulation well.

Effects of L-lysine and D-lysine on ε-Poly-L-lysine Biosynthesis and Their Metabolites by Streptomyces ahygroscopicus GIM8

Liu Shengrong,Wu Qingping,Zhang Jumei,Mo Shuping 한국생물공학회 2012 Biotechnology and Bioprocess Engineering Vol.17 No.6

ε-Poly-L-lysine (ε-PL), produced by Streptomyces or Kitasatospora strains, is a homo-poly-amino acid of Llysine,which is used as a safe food preservative. In this study, the effects of L-lysine and its isomer, D-lysine, on ε-PL biosynthesis and their metabolites by the ε-PLproducing strain Streptomyces ahygroscopicus GIM8 were determined. The results indicated that L-lysine added into the fermentation medium in the production phase mainly served as a precursor for ε-PL biosynthesis during the flask culture phase, leading to greater ε-PL production. At an optimum level of 3 mM L-lysine, a ε-PL yield of 1.16 g/L was attained, with a 41.4% increment relative to the control of 0.78 g/L. Regarding D-lysine, the production of ε-PL increased by increasing its concentrations up to 6 mM in the initial fermentation medium. Interestingly, ε-PL production (1.20 g/L) with the addition of 3 mM D-lysine into the initial fermentation medium in flasks was higher than that of the initial addition of 3 mM L-lysine (1.06 g/L). The mechanism by which D-lysine improves ε-PL biosynthesis involves its utilization that leads to greater biomass. After S. ahygroscopicus GIM8 was cultivated in the defined medium with L-lysine, several key metabolites, including 5-aminovalerate, pipecolate, and L-2-aminoadipate formed in the cells, whereas only L-2-aminoadipate was observed after D-lysine metabolism. This result indicates that Llysine and D-lysine undergo different metabolic pathways in the cells. Undoubtedly, the results of this study are expected to aid the understanding of ε-PL biosynthesis and serve as reference for the formulation of an alternative approach to improve ε-PL productivity using L-lysine as an additional substrate in the fermentation medium.

Hypoglycemic Effects of Ganoderma lucidum Polysaccharides in Type 2 Diabetic Mice

Chun Xiao,Qingping Wu,Xiao-Bing Yang,Wen Cai,Jian-Bin Tan,Jumei Zhang 대한약학회 2012 Archives of Pharmacal Research Vol.35 No.10

Our aims were to investigate the hypoglycemic effects and mechanisms of action of Ganoderma lucidum polysaccharides (GLPs) administered for 7 days in type 2 diabetic mice. The mice were randomly divided into four groups (8 mice/group): normal control group, diabetic control group, low-dose GLP-treated diabetic group (50 mg/kg/d), and high-dose GLP-treated diabetic group (100 mg/kg/d). Diabetes was induced by streptozotocin injection and high-fat dietary feeding. At the end of the study, fasting serum glucose, insulin, body weight (BW) and epididymal white adipose tissue weight were measured. The hepatic mRNA levels of glycogen phosphorylase (GP), fructose-1,6-bisphosphatase (FBPase), phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) genes were determined by real-time polymerase chain reaction. Both doses of GLPs significantly decreased fasting serum glucose, insulin and epididymal fat/BW ratio compared with the diabetic control group (p < 0.05). The hepatic mRNA levels of GP, FBPase, PEPCK and G6Pase were significantly lower in both GLP-treated groups compared with the diabetic control group. Taken together, GLPs significantly decrease fasting serum glucose levels in type 2 diabetic mice in a dose-dependent manner. The decreases in fasting serum glucose levels may be associated with decreased mRNA expression levels of several key enzymes involved in gluconeogenesis and/or glycogenolysis.

Classification and fatty acid composition analysis of Cronobacter spp. isolated from powdered infant formula in China

Yang, Xiaojuan,Wu, Qingping,Zhang, Jumei,Guo, Weipeng,Mo, Shuping,Liu, Shengrong 한국식품과학회 2016 Food Science and Biotechnology Vol.25 No.4

This study aimed to classify a collection of Enterobacter sakazakii (E. sakazakii) strains previously identified from powdered infant formula (PIF) to species level by recN gene sequencing and biochemical testing to determine the distribution of Cronobacter species in China and investigate the strain diversity by cellular fatty acid (CFA) analysis. Of 24 E. sakazakii isolates, 23 were identified as C. sakazakii and one was C. malonaticus. The 23 C. sakazakii isolates showed the same CFA profiles. The C. malonaticus isolate was discriminated from the C. sakazakii isolates by the significant difference in the amounts of $C_{12:0}$, $C_{14:0}$, and $C_{17:0\;cyclo}$ acids. These results showed that C. sakazakii and C. malonaticus were the common Cronobacter species distributed in PIF in China and that the isolates of the two species exhibited different CFA profiles. These findings are of value for epidemiological investigations and provide an alternative method for confirming various Cronobacter spp.

Development of a Virus Concentration Method and its Application for the Detection of Noroviruses in Drinking Water in China

Junyi Liu,Qingping Wu,Xiaoxia Kou 한국미생물학회 2007 The journal of microbiology Vol.45 No.1

A new procedure for the concentration of nonoviruses from water samples has been developed. This procedure (calcium flocculation-citrate dissolution method) uses the following steps: virus flocculation formed by treatment with 1 M CaCl2 and 1 M Na2HPO4, virus release by sodium citrate dissolution (0.3 M Na citrate, pH 3.5), and virus reconcentration by ultrafiltration. When reverse transcription (RT)-PCR was performed after the procedure, the overall detection sensitivity for seeded noroviruses in a one liter drinking water sample was as low as 1 RT-PCR unit, which is equal to a 10-6 dilution of the virus sample. This approach showed at least a 5-fold-higher sensitivity than the current method with its three steps of adsorption-elution-concentration. The newly developed procedure was used to test different brands of bottled drinking water from China for putative contamination with noroviruses. A total of 144 samples were analyzed; all of the samples were negative for norovirus specific nucleic acids.

Real-time PCR Targeting OmpA Gene for Detection of Cronobacter spp. in Powdered Infant Formula

Xiaohui Dong,Qingping Wu,Kui Wu,Jumei Zhang 한국식품과학회 2013 Food Science and Biotechnology Vol.22 No.2

Cronobacter spp. (formerly Enterobacter sakazakii), a pathogen commonly found in powdered infant formula (PIF), is a rare cause of invasive infection with a high mortality rate in neonates. In the present study, a realtime PCR assay was conducted to identify the pathogens in PIF using a TaqMan probe targeting the outer membrane protein A gene (ompA) of Cronobacter spp. The specificity of the PCR assay was tested against 25 strains of Cronobacter spp. and 38 non-Cronobacter bacterial species. The detection limits of this method are 1.0×102 copy/μL in standard plasmid, 1.1 CFU/100 g in PIF through 38 h of enrichment,and 2.8×102 CFU/mL in phosphate-buffered saline (pH 7.0). Based on the detection limits, real-time PCR is more sensitive than simplex and duplex PCR. These methods were successfully applied to actual samples, indicating that this real-time PCR assay can be used for the detection of Cronobacter spp. in PIF.

Rapid Detection of Noroviruses in Fecal Samples and Shellfish by Nucleic Acid Sequence-based Amplification

Xiaoxia Kou,Qingping Wu,Jumei Zhang,Hongying Fan 한국미생물학회 2006 The journal of microbiology Vol.44 No.4

The purpose of this study was to determine the efficacy of a nucleic acid sequence-based amplification (NASBA) method of detecting noroviruses in artificially and naturally contaminated shellfish. We used 58 fecal samples that tested positive for noroviruses with electron microscopy (EM) to develop an NASBA assay for these viruses. Oligonucleotide primers targeting the polymerase coding region were used to amplify the viral RNA in an isothermal process that resulted in the accumulation of RNA amplicons. These amplicons were detected by hybridization with digoxigenin-labeled oligonucleotide probes that were highly specific for genogroup I (GI) and genogroup II (GII) of noroviruses. The expected band of 327 bp appeared in denaturing agarose gel without any nonspecific band. The specific signal for each amplicon was obtained through Northern blotting in many repeats. All fecal samples of which 46 (79.3%) belonged to GII and 12 (20.6%) belonged to GI were positive for noroviruses by EM and by NASBA. Target RNA concentrations as low as 5 pg/ml were detected in fecal specimens using NASBA. When the assay was applied to artificially contaminated shellfish, the sensitivity to nucleic acid was 100 pg/1.5 g shellfish tissue. The potential use of this assay was also confirmed in naturally contaminated shellfish collected from different ponds in Guangzhou city of China, of which 24 (18.76%) out of 128 samples were positive for noroviruses; of these, 19 (79.6%) belonged to GII and 5 (20.4%) belonged to GI. The NASBA assay provided a more rapid and efficient way of detecting noroviruses in fecal samples and demonstrated its potential for detecting noroviruses in food and environmental samples with high specificity and sensitivity.

Rapid Detection of Noroviruses in Fecal Samples and Shellfish by Nucleic Acid Sequence-based Amplification

Kou Xiaoxia,Wu Qingping,Zhang Jumei,Fan Hongying The Microbiological Society of Korea 2006 The journal of microbiology Vol.44 No.4

The purpose of this study was to determine the efficacy of a nucleic acid sequence-based amplification (NASBA) method of detecting noroviruses in artificially and naturally contaminated shellfish. We used 58 fecal samples that tested positive for noroviruses with electron microscopy (EM) to develop an NASBA assay for these viruses. Oligonucleotide primers targeting the polymerase coding region were used to amplify the viral RNA in an isothermal process that resulted in the accumulation of RNA amplicons. These amplicons were detected by hybridization with digoxigenin-labeled oligonucleotide probes that were highly specific for genogroup I (GI) and genogroup II (GII) of noroviruses. The expected band of 327bp appeared in denaturing agarose gel without any nonspecific band. The specific signal for each amplicon was obtained through Northern blotting in many repeats. All fecal samples of which 46(79.3%) belonged to GII and 12(20.6%) belonged to GI were positive for noroviruses by EM and by NASBA. Target RNA concentrations as low as 5pg/ml were detected in fecal specimens using NASBA. When the assay was applied to artificially contaminated shellfish, the sensitivity to nucleic acid was 100pg/1.5g shellfish tissue. The potential use of this assay was also confirmed in naturally contaminated shellfish collected from different ponds in Guangzhou city of China, of which 24 (18.76%) out of 128 samples were positive for noroviruses; of these, 19 (79.6%) belonged to GII and 5 (20.4%) belonged to GI. The NASBA assay provided a more rapid and efficient way of detecting noroviruses in fecal samples and demonstrated its potential for detecting noroviruses in food and environmental samples with high specificity and sensitivity.