1.Characterization and Primer Design for Simple Sequence Repeat Loci in Salvia miltorrhiza Genome
Haibin XU ; Bo WANG ; Chao SUN ; Lifang XIE ; Jingyuan SONG
World Science and Technology-Modernization of Traditional Chinese Medicine 2013;(3):367-370
Salvia miltorrhiza Bge. is a perennial deciduous flowering plant. Its medicinal root and rhizomes part is widely used in the treatment of various diseases. In this study, bioinformatics analysis was performed to identify 4832 genome SSR loci with length longer than or equal to 40 bp from the draft genome assembly of S. miltorrhiza. The re-sults showed that the dinucleotide repeat motifs and trinucleotide repeat motifs constitute the main types of genome SSR loci, accounting for 37.3% and 61.3% respectively. SSR types enriched with A/T bases showed significantly higher abundance than other types, including AT/TA AAT/ATT, ATA/TAT, TAA/TTA, accounting for 30.5%, 21.6%, 17.1%, 20.4% of the total number of SSR loci, respectively. 1079 primer pairs were designed for these genome SSR loci. These primers can be used for genomic diversity analysis, genetic map construction, genetic marker screening. These data could lay the foundation for population genetics and genomics research of S. miltorrhiza.
2.RNA-Seq and genuine traditional Chinese medicine.
Xiaoyue WANG ; Jingyuan SONG ; Caixiang XIE ; Jianping HAN ; Shilin CHEN
Acta Pharmaceutica Sinica 2014;49(12):1650-7
RNA-Sequencing (RNA-Seq) is a newly-developed method in transcriptome research, it can afford more accurate transcription information and be more quickly by using Next-generation Sequencing (NGS) technology. RNA-Seq has been widely used in various biological fields. Genuine traditional Chinese medicines (TCM), with good quality and therapeutic effect, were always praised highly and used by famous physicians. The geo-herbalism formation of TCM is based on the product of the gene expression at specific space and time. So it has been a research hotspot to analyze the mechanism of biosynthesis through RNA-Seq in the study on the secondary metabolism of medicinal plant. This article mainly illustrates the RNA-Seq and its advantages, it also discusses the potential application in genuine TCM, and it can provide useful information for other researchers.
3.Effects of main post combined with auxiliary pile on the fracture resistance of the flat-shaped residual roots
Meng HAN ; Qiong DU ; Jing XIE ; Jingyuan LIU ; Xiao ZHANG
Journal of Practical Stomatology 2015;(4):582-584
20 first mandibular premolars were randomly divided into 2 groups(n =10).The teeth in experimental group were treated by fi-ber main post in combination with auxiliary pile,in control group by single fiber main post,and then were restored by metal crown.They were fixed in universal testing machine.The fracture load(N)of experimental and control group was (846.50 ±40.33)and (437.90 ±41.15) respectively(P <0.01).
4.Analysis of association between γ-glutamyltransferase and risk of metabolic syndrome in health checkup cohort
Jingyuan XIE ; Haibin ZHOU ; Wengao ZHAO ; Zhenshan LEI
Chinese Journal of Health Management 2015;(3):182-185
Objective To analyze the relationship between baseline serum γ?glutamyltransferase (GGT) and risk of the metabolic syndrome (MS). Method A total of 4 935 adults from health checkup population in Shenzhen were enrolled into a 10?year follow?up study, of these adults 81.84%were male and 18.16% were female, the average age was 60.54 ± 10.38 years.The follow?up outcome measure was the occurrence of MS. The proportional hazards model was adopted to calculate the hazard ratios (HR) and 95%confidence intervals (95%CI) to analyze the association of GGT with the development of MS. Reslut The mean follow up period was 5.0 ± 2.9 years, and there were 24 713 person?years of follow?up, and 1 689 subjects developed MS. During the follow?up, the cumulative incidence and incidence density of MS were 34.22%and 68.34/1 000 person?years, respectively. For both genders, the association between GGT and MS presented dose?response relationship trend (male: M?C χ2=32.78, P<0.001; female: M?C χ2=18.80, P<0.001). After adjusting for age, gender, body mass index, systolic blood pressure, diastolic blood pressure, high?density lipoprotein cholesterol, low?density lipoprotein cholesterol, triglycerides, uric acid and fasting blood glucose in Cox regression model, the HR for MS in quartiles 3 and 4 level of GGT was 1.45 (95%CI:1.08-1.85) and 1.52 (95%CI:1.15-1.99), respectively. Conclusion The GGT level could be an important risk factor and predictor for the development of MS.
5.Correlation of the serum S100βprotein level with early postoperative cognitive dysfunction in infants after propofol or etomidate anesthesia
Yihong JIANG ; Jingyuan XIE ; Weiwei XIONG ; Zhihua HUANG ; Aiguo LI ; Yi TAN ; Lingyun PENG
Journal of Medical Postgraduates 2015;(8):824-828
Objective There is a lack objective methods for the diagnosis of postoperative cognitive dysfunction (POCD).This study aimed to investigate the influence of propofol or etomidate anes-thesia on the postoperative cognitive function and serum S 100βprotein level in infants . Methods This study included 100 hernia infants aged 1-3 years treated by laparoscopic herniorrhaphy under propofol (n=50) or etomidate anesthesia (n=50).At 1 day before and 3 days after surgery, we assessed the cognitive function of the patients using Bayley Scales of Infant and Toddler Development ( BSID-Ⅲ) and further divided each group into a POCD and a non-POCD sub-group based on the results of diagnosis made according to the Z-scores.Using ELISA, we measured the levels of the serum S100βpro-tein in the iliac venous blood drawn preoperatively ( T0 ) and before PACU ( T1 ) and compared them between the POCD and non-POCD groups. Results At 3 days after operation, POCD was observed in 10 cases (20.0%) in the propofol group and 9 cases (18.0%) in the etomidate group, with no statistically significant differences between the two (P>0.05).The level of the serum S100βprotein was markedly elevated in both the propofol and etomidate groups at T 1 as compared with that at T0(P<0.05), and so was it in the POCD in comparison with that in the non-POCD group (P<0.05), with no statistically significant differences between the two groups at T1(P>0.05).A significant correlation was found between the postoperative S 100βlevel and POCD at 3 days after surgery in both the propofol (r=0.842, P=0.001) and the etomidate group (r=0.821, P=0.001). Conclusion Propofol and etomidate anes-thesia can induce different degrees of postoperative decline of cognitive function in 1-3 years old infants .The post-anesthesia elevation of the serum S100βprotein level is positively correlated with early postoperative POCD and indicates various degrees of brain damage .
6.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 .
7.Contrucion of Salvia miltorrhiza Protein/Peptide Database for Mass Spectrometry Analysis
Haibin XU ; Jingyuan SONG ; Jun QIAN ; Bo WANG ; Lifang XIE ; Hongmei LUO
World Science and Technology-Modernization of Traditional Chinese Medicine 2013;(3):339-341
Salvia miltorrhiza Bge is a medicinal herb in traditional Chinese medicines. Until recently, dozens of compound ingredients with medicinal properties have been identified from S. miltorrhiza. Proteome analysis on medicinal ingredients synthesis mechanisms could provide a theoretical basis for S. miltorrhiza genetic improve-ment. In this study, a S. miltorrhiza specific protein/peptide sequence database was constructed using Illumina high-throughput transcriptome sequencing data of multiple types of S. miltorrhiza tissues. The database could act as a key component to carry out the proteome analysis in S. miltorrhiza.
8.Universality Assessment of matK Primer Pairs in Seed Plants
Linchun SHI ; Jinxin LIU ; Hui YAO ; Xiaolan XU ; Tianyi XIN ; Caixiang XIE ; Jingyuan SONG
World Science and Technology-Modernization of Traditional Chinese Medicine 2013;(3):381-386
matK is one of the core DNA barcode markers for plant DNA barcode identification and its universality using single makers has been in controversy. However, the universalities of different matK primer pairs in same seed plant group (order) and same matK primer pairs in different seed plant groups (order) are lack of systematic research. In this study, we collected 14563 full-length matK sequences of 11429 species of 3292 genera in 239 families belonging to 36 orders in seed plants. The universalities of 13 matK primer pairs and its 78 primer com-binations have been assessed using bioinformatics methods. The results indicated that xf/5r, 1F/8R, 390F/1326R and 3F_KIM/1R_KIM were the four most universality primer pairs. The four markers' universalities were 91.18%, 84.65%, 79.81% and 80.94% respectively in all 11429 seed plants. The most universality primer pairs in different orders were different. For each order, the primer pair with maximum universality was different. the xf/5r was the basal primer pair for primer combination and 1F/8R, 1F/1R, M3/M4 and 3F_KIM/1R_KIM could be the complementary primer pairs. This study could be a valuable resource for the primer selection of the research DNA barcoding identification in seed plants.
9.Comparative study of continuous ambulatory peritoneal dialysis and hemodialysis on polycystic kidney disease patients
Jingyuan XIE ; Nan CHEN ; Hong REN ; Xiaonong CHEN ; Wen ZHANG ; Jing XU ; Ping ZHU
Chinese Journal of Nephrology 2009;25(2):101-105
Objective To compare the efficacy of continuous ambulatory peritoneal dialysis (CAPD) and hemodialysis (HD) on polycystic kidney disease (PKD) patients with end-stage renal disease (ESRD). Methods Retrospective analysis was made on 29 patients with PKD who carded out dialysis therapy for over 3 months in our department from January 2001 to December 2007. They were divided into the CAPD group (10 cases, 34.5%) and HD group (19 cases, 65.5%). Ten cases of non-PKD CAPD patients were randomly selected as the control, who matched the CAPD group in terms of age and gender. The patient information was recorded, such as general data, initial dialysis data, comphcations, survival time, quit of dialysis or death, etc. Kaplan-Meier method and Log-rank test were adopted to analyze the survival rate. Results The survival rates of 1-, 3- and 5-year for the CAPD group were 90%, 75% and 25% respectively, while for the HD group were 94.4%, 67.6%, and 48.3%, and for the control were 83.3%, 44.4% and 22.2% respectively, with no significant differences among 3 groups (P>0.05). group and the control were quite similar. The incidence of peritonitis for the CAPD group (0.62 times/patient year) was similar to that for the control (0.30 times/patient year)(P>0.05). The duration of the lust peritonitis[(23.5±4.0) months vs (20.0±15.8) months] and the catheter exit-site infection (0 time vs 1 time) for two groups were similar as well (P>0.05). One patient had hernia in CAPD group and no patient in control group had hernia. The incidence of peritoneal dialysate leakage was similar between these two groups. In the HD group, two patients (10.5%) had cerebral hemorrhage resulting in death, and 10 patients (52.6%) had cystic hemorrhage, 5 out of whom underwent operation due to repeated cystic hemorrhage and 2 cases received unilateral nephrectomy because of severe hemorrhage. No patient in CAPD group had cerebral hemorrhage but 1 patient (10%) had cystic hemorrhage and recovered after conservative treatment. The hemorrhage complication incidence of CAPD group was significantly lower than that of HD group (P<0.05). Conclusions The prognosis and complication incidence in PKD and non-PKD patients treated with CAPD are similar. The prognosis of PKD patients treated with CAPD or HD is also similar, and the risk of hemorrhage complications of PKD patients treated with CAPD may be decreased compared with those treated with HD. PKD patients can choose HD or PD as the initial therapy of ESRD unless existence of hernia or intolerance. PKD is not the contraindication of PD.
10.Prospective efficacy comparison between the two-cuff swan neck catheter and the Tenckhoff catheter in peritoneal dialysis patients
Jingyuan XIE ; Ping ZHU ; Pingyan SHEN ; Hong REN ; Xiaomin HUANG ; Xiao LI ; Xiaonong CHEN ; Nan CHEN
Chinese Journal of Nephrology 2008;24(10):685-689
Objective To compare the efficacy between the two-cuff swan neck catheter and the Tenckhoff catheter in continuous ambulatory peritoneal dialysis (CAPD) patients prospectively. Methods One hundred and ten patients with end-stage renal disease (ESRD) were selected as candidates, who received catheter implantation and CAPD therapy for the first time. Patients were divided into group A (swan neck catheter group) and group B (Tenckhoff catheter group), 55 patients for each group. Catheters of beth groups had a straight end and were implanted by routine surgical procedure. One-year follow-up was performed and information was recorded such as complications, survival time, quit of dialysis, death, etc. Survival analysis was carried out by Kaplan-Meier method and Log-Rank tests. Results At the end of follow-up, 17 patients died, 3 received renal transplantation, 8 were transferred to hemodialysis, 3 went to other hospitals, and 79 patients (71.8%) remained in our department for CAPD. Twenty-six patients of both groups had peritonitis with a total of 35 occurrences. The total incidence of peritonitis was 0.32 times/patient year, with the detailed figure of 0.35 times/patient year for group A and 0.29 times/patient year for group B respectively (P0.05). The time interval between the catheter implanting and the onset of peritonitis was (30±29) weeks and (29±24) weeks for group A and group B respectively (P0.05). The risk of developing peritonitis in both groups was 26.97% within 1 year. Tunnel infection occurred in 2 patients and exit-site infections in 9 patients of two groups. The incidence of tunnel plus exit-site infections was 0.1 times/patient year. Incidence of tunnel infection and the exit-site infection for group A was lower than that of group B (0 vs 0.036 times/patient year and 0.06 times/patient year vs 0.11 times/patient year respectively). However, the difference was not significant (P0.05). Mechanical complications of catheter (catheter migration, omcntum wrapping, leakage of peritoneal dialysates, slip out of outer cuff), incidence of inguinal hernia and bellyache between two groups were not significantly different (P0.05). There were 4 cases of catheter drawing in each group. Both two groups had the same 12-month technical survival rate as 92.73%. Of 17 dead cases, 7 were in group A and 10 in group B (P0.05). The main death causes were cardiocerebral events (47.1%) and infections (23.5%). The 12-month survival rate was 86.34% for group A and 80.68% for group B (P0.05). Conclusions There are no significant differences of infection, mechanical complications, technical survival rate and patients' survival rate between two groups. The efficacy of swan-neck catheter is similar to Tenckhoff catheter in CAPD patients.