1.ITS2 Sequences as Barcodes for Identifying and Analyzing Pseudolaricis Cortex
Ting GAO ; Xunzhi ZHU ; Jingyuan SONG
World Science and Technology-Modernization of Traditional Chinese Medicine 2013;(3):387-392
Pseudolaricis Cortex and its adulterants were identified using DNA barcoding technique in this study. The sequences of ITS2 of Pseudolaricis Cortex and its five adulterants including 37 samples were analyzed. Se-quences were assembled using CodonCode Aligner 3.5.7. K2P distances were calculated and NJ tree was per-formed applying MEGA5.0. The ITS2 secondary structure was predicted using the ITS2 database and website. The results showed that the haplotypes of ITS2 regions of Pseudolaricis Cortex were the same as that of the original plant leaves. The inter-specific K2P distances of ITS2 were obviously higher than the intra-specific ones. Sam-ples of Pseudolaricis Cortex were clustered into a single clade in the NJ tree. The secondary structure of ITS2 of Pseudolaricis Cortex was significantly different from its adulterants. Therefore, ITS2 could powerfully discriminate Pseudolaricis Cortex and its adulterants.
2.Comparative studies on codon usage bias of Ganoderma lucidum based on analysis of genomic and transcriptomic data.
Xiaoxuan ZHU ; Yingjie ZHU ; Jingyuan SONG ; Chao SUN ; Shilin CHEN
Acta Pharmaceutica Sinica 2014;49(9):1340-5
Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, because the genome sequences of higher organisms are still not available up to now. In this study, we found that we could obtain the same optimal codons of Ganoderma lucidum (Curtis: Fr.) P. Karst based on its whole genomic data or large-scale transcriptomic data from its liquid-cultured hyphae, primordium and fruiting body, separately. This result indicated the feasibility to understand the codon usage bias based on the large-scale transcriptomic data. By calculating the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 26 terpene synthases (TS) of G. lucidum, we found that the rare codons of S. cerevisiae have a higher proportion in TS genes, while the rare codons of E. coli have relatively lower, suggesting that the TS genes of G. lucidum are possibly more difficult to be expressed in S. cerevisiae than in E. coli. Chemical synthesis of TS genes according to the yeast optimal codons will be an effective way to solve the problem on the mismatch of gene codon bias between the foreign genes and the host strain.
3.Analysis on mar gene mutation in mult-drug resistant Shigella
Ruili Lü ; Guangcai DUAN ; Yuanlin XI ; Jingyuan ZHU
Chinese Journal of Microbiology and Immunology 2008;28(3):208-211
Objective To study the association of multi-drug resistance with mutations in mar gene in clinical isolates of Shigella.Methods Fifty-four clinical isolates of Shigella were collected.Susceptibility tests of tetracycline(TE),chloramphenieol(C),ampicillin(AM),cipr ofloxacin(CIP),and norfloxacin(NOR)were performed in a11 isolates.Hexane and cyclohexane were used to study the organic solvent tolerance of all clinical isolates.marOR genes of these strains were analyzed by potymerase chain reaction-single strand conformation polymorphism(PCR-SSCP)and were sequenced. Results Thirty-five multi-drug resistant strains were identified,and the rate of multi-drug resistance was 64.8%.Thirty-eight of 54 strains were tolerant to organic solvent,including 33 multi-drug resistance strains,3 drug resistant strains and 2 sensitive strains. marOR gene was found in all strains by PCR, and 5 multi-drug resistant strains,(14.29%)carrying marOR gene mutations in multi-drug resistant strains were found by SSCP analysis.DNA sequence analysis of marOR gene revealed that there was a 4 base deletion from base 1376 to 1379 in marO gene that resulted in frame-shift mutation.However,this deletion mutation didn;t exist in the standard strain S51250 and sensitive strains.There were 10 point mutations of marR gene in multi-drug resistant strains,2 of them resulting in amino acid changes:1752(G→A)Gly→ser,1854(T→c)Tyr→His.The rest mutations were all nonsense,and some of them occurred in sensitive strains or in many other strains.Conclusion The marO gene mutation may play an important role in the regulation of multi-drug resistance in Shigella spp.
4.ADAR2 inhibits MAVS expression by editing its 3'UTR in cells
Tao LI ; Jingyuan LI ; Xilin ZHU ; Xiaopan WU ; Ying LIU
Basic & Clinical Medicine 2017;37(6):747-751
Objective To investigate the effect of ADAR2 on the expression of MAVS and its mechanism.MethodsThe RT-qRCR was used to detect the expression of ADAR gene family, the expression level of ADAR2 and MAVS in cells.The effect of ADAR2 on the 3'UTR region of MAVS was detected by Pyrosequencing.To detect the expression of luciferase by dual luciferase reporter plasmid assay;The expression of ADAR2 and MAVS were detected by Western blot.Results In the ADAR family, the abundance of ADAR1 was the highest, followed by ADAR2, but the expression of ADAR3 was poor, which was almost impossible to detect(P<0.05).ADAR2 played a critical role in RNA editing of chr20:3869744 sites on the 3'UTR region of MAVS(P<0.001).On the 3'UTR editing site of MAVS, the luciferase activity of the edited G allele was significantly lower than that of the normal A allele(P<0.01).At the level of transcription and translation, ADAR2 significantly inhibited the expression of MAVS(P<0.05).Conclusions ADAR2 by editing MAVS` 3'UTR on the chr20:3869744 site, which makes the occurrence of A to G replacement, inhibits the expression of MAVS.
5.The effect of extracellular signal-regulated kinases signaling pathway inhibition on histone phosphorylation and gene expression in colorectal canoer cells
Wenying LI ; Ting YE ; Hongyin ZHU ; Yingxuan CHEN ; Jingyuan FANG
Chinese Journal of Digestion 2010;30(5):317-321
Objective To study the effects of extracellular-signal regulated kinase mitogenactivated protein kinase (ERK-MAPK) signaling pathway inhibition on histone phosphorylation and the related gene expression in human colorectal cancer cells.Methods Two human colorectal cancer cell lines (SW1116 and HCT116) were cultured and treated with gradient(0,20,40/μmol/L) doses of ERK-MAPK signaling pathway inhibitor U0126.Cell viability was determined by cell counting kit 8 (CCK-8) assay.Cell cycle distribution was assessed by flow cytometry.The expression levels of histone H3 kinases including ribosomal S6 serine-threonine kinase (RSK-2) and mitogen-and stressactivated protein kinase 1 and 2 (MSK1 and MSK2),and the levels of histone H3 (Ser10) phosphorylation and c-Fos protein were detected using Western blotting.Results Treatment of these two human colorectal cancer cell lines with ERK-MAPK inhibitor resulted in a time and dose-dependent inhibition of cell proliferation significantly. Proliferation rate of HCT116 was reduced to 47% at 72 hours after 40/μmol/L U0126 treatment. Cell cycle analysis showed that the percentage of phase G0/G1 cells significantly increased (P<0. 01) and the percentage of phase S cells decreased (P<0.01) after treatment with ERK-MAPK inhibitor. The expression of MSK1 and RSK2 reduced obviously in both of human colorectal cancer cell lines treated with U0126, which resulted in a 28% and 40% reduction of levels of MSK1 and RSK2 as compared with control HCT116 cells respectively,while no detectable change in the expression of MSK2 was found. Consistent with this, the expression level of histone H3 (ser10) phosphorylation was markedly down-regulated by ERK-MAPK inhibitor, and the related protein c-Fos expression decreased accordantly. Conclusions Decreased ERK-MAPK signaling pathway may reduce histone H3 (Ser10) phosphorylation via suppression of the activity of histone H3 kinase including MSK1 and RSK2, but not MSK2, consequently decrease the expression of c-Fos protein, which results in the inhibition of colorectal cancer cells proliferation.
6.Progress of unilateral breast cancer undergoing contralateral prophylactic mastectomy
Kaiwen SHEN ; Jingyuan ZHU ; Ximing GU ; Jie WANG ; Longdi YAO
International Journal of Surgery 2021;48(3):190-194
A growing number of people with unilateral breast cancer have chosen to undergo contralateral prophylactic mastectomy in order to prevent the occurrence of second primary breast cancer and thus avoid associated treatment and death. Contralateral prophylactic mastectomy has been considered beneficial in high-risk populations, such as premenopausal BRCA1/2 mutation carriers. As a result, contralateral prophylactic mastectomy acceptance in patients with no such mutation is controversial. Contralateral prophylactic mastectomy can reduce the risk by up to 95%. Therefore, it is very important to evaluate the risk of contralateral breast cancer and to make appropriate surgical treatment. A review of risk factors for contralateral breast cancer and the benefits of contralateral prophylactic mastectomy in patients with unilateral breast cancer is presented.
7.The evaluation of on-line hemodiafiltration in acute cerebrovascular disease patients complicated with hyperosmolar nonketotic diabetic coma
Xianghong ZHU ; Dingshi LUO ; Zhengli QUAN ; Juhong YANG ; Wangshan CHEN ; Xuexiang ZHENG ; Jingyuan YANG ; Yanfang WANG
Chinese Journal of Emergency Medicine 2008;17(7):693-695
Objective To access evaluate the efficacy and safety of on-line hemodiafiltration for treating a-cute cerebrovascular disease (ACVD) patients complicated with hyperosmolar nonketotie diabetic coma (HNDC).Method Totally 11 patients of ACVD complicated with HNDC were observed for this prospective control study.All of them underwent on-line hemodiafiltrafion for 90 minutes using Fressnius 4008S Hemodialysis Machine withONLILNEplus TM and F60 one hour after final diagnosis was made. The bicarbonate ultrafiltrate rate was set at 500ml/min and blood flow at 150 ~ 180 ml/min; and the substitute fluid were infused with post-dilution at 50 ~ 60ml/min. The symptom of brain edema and cardiac insufficiency during the same course of treatment was observed.Blood were taken from the patients to detect serum kalium, serum glucose, serum natrium, BUN and plasma os-motic pressure at one hour before treatment and six hours after treatment, respectively. The change of in conscious-ness and adverse effects were evaluated at 24 hours after treatment. Results All patients were treated successful-ly. The blood glucose, serum natrium, serum kalium, BUN and plasma osmotic pressure were decreased after on-line hemodiafiltration. Among the 11 patients, consciousness was improved obviously in 8 patients, 3 patientsdied, accounting for 73% of successful effectiveness. Conclusions The on-line hemodiafiltration was effectiveand safe for treating ACVD patients complicated with HNDC.
8.Psychological assessment and research to the wounded of 96 cases in Yushu,Qinghai
Shiyuan TANG ; Shuheng ZHU ; Hongyu LONG ; Jingyuan HUANG ; Luren PANG ; Yu CAO
Chinese Journal of Emergency Medicine 2010;19(6):640-642
Objective Provided the basis on psychological treatment for the earthquake wounded, through investigated the psychological healthy condition of them in Yushu, Qinghai Province. Method To investigated the 102 cases earthquake wounded from 15 - 18 April 2010 who transported from Yushu, Qinghai to West China hospital of Sichuan University; Accept standard: The wounded (96 cases) who could cooperated this investigative; Adopted the Hamiton anxiety scale( HAMA) to had a review investigation for the wounded in the from of talk, and used the SPSS statistics software to have the Wilcoxon Mann-Whitney test and correlation analysis for the investigation data. Results There were 55 of the 96 cases have been confirmed anxiety, HAMA > 14 points; 16 cases had serious anxiety (HAMA > 29 points); The average score in all of them equal to (17.3 ±10.8) points. And there was a remarkable difference between male and female. The age is possible have related degree with the wounded anxious. What the main in their characteristics of them was Psychic anxiety. Conclusions There was apparent anxiety of them whom came from Yushu, Qinghai, and they needed proactive psychological treatment, female、 middle-aged and elderly need more.
9.DNA barcoding the medicinal plants of the genus Paris.
Yingjie ZHU ; Shilin CHEN ; Hui YAO ; Rui TAN ; Jingyuan SONG ; Kun LUO ; Jing LU
Acta Pharmaceutica Sinica 2010;45(3):376-82
DNA barcoding is a technique in which species identification and discovery are performed by using short and standard fragments of DNA sequences. In this study, eleven species of Paris, including seven varieties, were sampled. Five chloroplast sequences, psbA-trnH, rpoB, rpoC1, rbcL, matK, and one nuclear marker, the second internal transcribed spacer (ITS2) of ribosomal DNA, were amplified and sequenced. The PCR amplification and sequencing efficiency, intra- and inter-specific divergence and barcoding gap were used to evaluate different loci, and the identification efficiency was assessed using BLAST1 and Nearest Distance methods. The ITS2 sequences in the studied samples of Paris were amplified and sequenced successfully using primers designed by our group, while matK showed low level in the amplification and psbA-trnH was difficult for sequencing because of over 800 bp and poly (A) structure. Analysis of the intra- and inter-specific divergence and barcoding gap showed ITS2 was superior to other loci. The ITS2 showed a much higher percentage of success (100%) in identification than other five loci, none of which indicated more than 50% except matK (52.9%). The 2-locus combination of rbcL+matK didn't improve ability of authentication. In addition, the rate of successful identification with ITS2 kept 100% when the samples were expanded to 67 samples of 29 species. In conclusion, ITS2 can be used to correctly identify medicinal plants of Paris, and it will be a potential DNA barcode for identifying medicinal plants of other taxa.
10.Clinical significance of histological examination and noninvasive measurements in renal osteodystrophy
Ping ZHU ; Jiajun WU ; Guanyu WANG ; Ying QIAN ; Jin QI ; Zhidong GU ; Jingyuan XIE ; Nan CHEN
Chinese Journal of Nephrology 2008;24(5):309-314
Objective To analyze the histological changes of bone diseases and to investigate the noninvasive measurements for diagnosing renal osteodystrophy (ROD) in maintenance dialysis patients . Methods Ninety-one patients were selected to receive bone biopsy . The bone samples were stained with HE, toluidine blue and Masson, and were examined with light microscopy . The levels of immunoreactive parathyroid hormone (iPTH), osteoprotegerin (OPG),sRANKL and osteocalcin (OCN) were determined in the patients enrolled from 2004 to 2006 . The level of iPTH was measured by radioimmunoassay . OPG and sRANKL were measured by ELISA,and OCN was measured by chemiluminescence . Results The incidence of ROD in the maintenance patients was 100% . According to the histological appearance, 50 cases (54 .9%) were high turnover bone disease (secondary hyperparathyroid bone disease), 9 cases (9 .9%) were low turnover bone diseases(osteomalacia and adynamic bone disease), and 32 cases(35 .2% ) were mixed bone disease . The level of iPTH in patients with ROD was significantly increased compared with healthy controls . It was the lowest in low turnover bone diseases . There was no difference among three types of ROD . OPG level was significantly increased compared with healthy controls [(2176 .58±1576 .08) pmol/L vs (1310 .46±1254 .00) pmol/L, P<0 .05] . The level in high turnover bone diseases was higher than that of the healthy controls [(2261 .85±1712 .22) pmol/L vs (1310 .46±1254 .00) pmol/L, P<0 .05] . There was no difference among three types of ROD .sRANKL level in high turnover bone disease was significantly increased compared with healthy controls [(0 .328±0 .524)pmol/L vs (0 .084±0 .190) pmol/L, P<0 .05] . OCN level was also higher than that of the healthy controls (P<0 .05), and the OCN level in low turnover ROD was the lowest among three types of ROD . OCN level in mixed ROD was dramatically increased as compared to low turnover ROD [(226 .633±66 .455) pmol/L vs (193 .03±104 .269) pmol/L, P <0 .05] .Conclusions The histological changes of bone disease can be indicated by iPTH level, but the types of ROD can not be distinguished according to iPTH level neither be differentiated by the levels of OPG, sRANKL and OCN . Bone histomorphometry is still the golden standard for diagnosing renal osteodystrophy .