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1.  Dynamic changes of HBV markers and HBV DNA load in infants born to HBsAg(+) mothers: can positivity of HBsAg or HBV DNA at birth be an indicator for HBV infection of infants? 
BMC Infectious Diseases  2013;13:524.
Neither HBV DNA nor HBsAg positivity at birth is an accurate marker for HBV infection of infants. No data is available for continuous changes of HBV markers in newborns to HBsAg(+) mothers. This prospective, multi-centers study aims at observing the dynamic changes of HBV markers and exploring an early diagnostic marker for mother-infant infection.
One hundred forty-eight HBsAg(+) mothers and their newborns were enrolled after mothers signed the informed consent forms. Those infants were received combination immunoprophylaxis (hepatitis B immunoglobulin [HBIG] and hepatitis B vaccine) at birth, and then followed up to 12 months. Venous blood of the infants (0, 1, 7, and 12 months of age) was collected to test for HBV DNA and HBV markers.
Of the 148 infants enrolled in our study, 41 and 24 infants were detected as HBsAg(+) and HBV DNA(+) at birth, respectively. Nine were diagnosed with HBV infection after 7 mo follow-up. Dynamic observation of the HBV markers showed that HBV DNA and HBsAg decreased gradually and eventually sero-converted to negativity in the non-infected infants, whereas in the infected infants, HBV DNA and HBsAg were persistently positive, or higher at the end of follow-up. At 1 mo, the infants with anti-HBs(+), despite positivity for HBsAg or HBV DNA at birth, were resolved after 12 mo follow-up, whereas all the nine infants with anti-HBs(−) were diagnosed with HBV infection. Anti-HBs(−) at 1 mo showed a higher positive likelihood ratio for HBV mother-infant infection than HBV DNA and/or HBsAg at birth.
Negativity for anti-HBs at 1 mo can be considered as a sensitive and early diagnostic indictor for HBV infection in the infants with positive HBV DNA and HBsAg at birth, especially for those infants with low levels of HBV DNA load and HBsAg titer.
PMCID: PMC3829094  PMID: 24195671
2.  The Genomes of Oryza sativa: A History of Duplications 
Yu, Jun | Wang, Jun | Lin, Wei | Li, Songgang | Li, Heng | Zhou, Jun | Ni, Peixiang | Dong, Wei | Hu, Songnian | Zeng, Changqing | Zhang, Jianguo | Zhang, Yong | Li, Ruiqiang | Xu, Zuyuan | Li, Shengting | Li, Xianran | Zheng, Hongkun | Cong, Lijuan | Lin, Liang | Yin, Jianning | Geng, Jianing | Li, Guangyuan | Shi, Jianping | Liu, Juan | Lv, Hong | Li, Jun | Wang, Jing | Deng, Yajun | Ran, Longhua | Shi, Xiaoli | Wang, Xiyin | Wu, Qingfa | Li, Changfeng | Ren, Xiaoyu | Wang, Jingqiang | Wang, Xiaoling | Li, Dawei | Liu, Dongyuan | Zhang, Xiaowei | Ji, Zhendong | Zhao, Wenming | Sun, Yongqiao | Zhang, Zhenpeng | Bao, Jingyue | Han, Yujun | Dong, Lingli | Ji, Jia | Chen, Peng | Wu, Shuming | Liu, Jinsong | Xiao, Ying | Bu, Dongbo | Tan, Jianlong | Yang, Li | Ye, Chen | Zhang, Jingfen | Xu, Jingyi | Zhou, Yan | Yu, Yingpu | Zhang, Bing | Zhuang, Shulin | Wei, Haibin | Liu, Bin | Lei, Meng | Yu, Hong | Li, Yuanzhe | Xu, Hao | Wei, Shulin | He, Ximiao | Fang, Lijun | Zhang, Zengjin | Zhang, Yunze | Huang, Xiangang | Su, Zhixi | Tong, Wei | Li, Jinhong | Tong, Zongzhong | Li, Shuangli | Ye, Jia | Wang, Lishun | Fang, Lin | Lei, Tingting | Chen, Chen | Chen, Huan | Xu, Zhao | Li, Haihong | Huang, Haiyan | Zhang, Feng | Xu, Huayong | Li, Na | Zhao, Caifeng | Li, Shuting | Dong, Lijun | Huang, Yanqing | Li, Long | Xi, Yan | Qi, Qiuhui | Li, Wenjie | Zhang, Bo | Hu, Wei | Zhang, Yanling | Tian, Xiangjun | Jiao, Yongzhi | Liang, Xiaohu | Jin, Jiao | Gao, Lei | Zheng, Weimou | Hao, Bailin | Liu, Siqi | Wang, Wen | Yuan, Longping | Cao, Mengliang | McDermott, Jason | Samudrala, Ram | Wang, Jian | Wong, Gane Ka-Shu | Yang, Huanming | Bennetzen, Jeff
PLoS Biology  2005;3(2):e38.
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes
PMCID: PMC546038  PMID: 15685292
3.  An Exploratory Study of the Association between KCNB1 rs1051295 and Type 2 Diabetes and Its Related Traits in Chinese Han Population 
PLoS ONE  2013;8(2):e56365.
Since the KCNB1 encoding Kv2.1 channel accounts for the majority of Kv currents modulating insulin secretion by pancreatic islet beta-cells, we postulated that KCNB1 is a plausible candidate gene for genetic variation contributing to the variable compensatory secretory function of beta-cells in type-2 diabetes (T2D). We conducted two studies, a case-control study and a cross-section study, to investigate the association of common single-nucleotide polymorphisms (SNPs) in KCNB1 with T2D and its linking traits. In the case-control study, we first examined the association of 20 tag SNPs of KCNB1 with T2D in a population with 226 T2D patients and non-diabetic subjects (screening study). We then identified the association in an enlarged population of 412 T2D patients and non-diabetic subjects (replication study). In the cross-sectional study, we investigated the linkage between the candidate SNP rs1051295 and T2D by comparing beta-cell function and insulin sensitivity among rs1051295 genotypes in a general population of 1051 subjects at fasting and after glucose loading (oral glucose tolerance tests, OGTT) in 84 fasting glucose impaired subjects, and several T2D-related traits. We found that among the 19 available tag SNPs, only the KCNB1 rs1051295 was associated with T2D (P = 0.027), with the rs1051295 TT genotype associated with an increased risk of T2D compared with genotypes CC (P = 0.009). At fasting, rs1051295 genotype TT was associated with a 9.8% reduction in insulin sensitivity compared to CC (P = 0.008); along with increased plasma triglycerides (TG) levels (TT/CC: P = 0.046) and increased waist/hip (W/H) ratio (TT/CC: P = 0.013; TT/TC: P = 0.002). OGTT confirmed that genotype TT exhibited reduced insulin sensitivity by 16.3% (P = 0.030) compared with genotype TC+CC in a fasting glucose impaired population. The KCNB1 rs1051295 genotype TT in the Chinese Han population is associated with decreased insulin sensitivity and increased plasma TG and W/H ratio, which together contribute to an increased risk for T2D.
PMCID: PMC3576392  PMID: 23431371
4.  Straw Mulching Reduces the Harmful Effects of Extreme Hydrological and Temperature Conditions in Citrus Orchards 
PLoS ONE  2014;9(1):e87094.
Extreme weather conditions with negative impacts can strongly affect agricultural production. In the Danjiangkou reservoir area, citrus yields were greatly influenced by cold weather conditions and drought stress in 2011. Soil straw mulching (SM) practices have a major effect on soil water and thermal regimes. A two-year field experiment was conducted to evaluate whether the SM practices can help achieve favorable citrus fruit yields. Results showed that the annual total runoff was significantly (P<0.05) reduced with SM as compared to the control (CK). Correspondingly, mean soil water storage in the top 100 cm of the soil profile was increased in the SM as compared to the CK treatment. However, this result was significant only in the dry season (Jan to Mar), and not in the wet season (Jul to Sep) for both years. Interestingly, the SM treatment did not significantly increase citrus fruit yield in 2010 but did so in 2011, when the citrus crop was completely destroyed (zero fruit yield) in the CK treatment plot due to extremely low temperatures during the citrus overwintering stage. The mulch probably acted as an insulator, resulting in smaller fluctuations in soil temperature in the SM than in the CK treatment. The results suggested that the small effects on soil water and temperature changes created by surface mulch had limited impact on citrus fruit yield in a normal year (e.g., in 2010). However, SM practices can positively impact citrus fruit yield in extreme weather conditions.
PMCID: PMC3904954  PMID: 24489844
5.  Epidemiology of general obesity, abdominal obesity and related risk factors in urban adults from 33 communities of northeast china: the CHPSNE study 
BMC Public Health  2012;12:967.
Obesity increases the risk of many diseases. However, there has been little literature about the epidemiology of obesity classified by body mass index (BMI) or waist (abdominal obesity) among urban Chinese adults. This study is to fill the gap by assessing the prevalence of obesity and associated risk factors among urban Chinese adults.
A representative sample of 25,196 urban adults aged 18 to 74 years in Northeast China was selected and measurements of height, weight and waist circumference (WC) were taken from 2009–2010. Definitions of overweight and obesity by the World Health Organization (WHO) were used.
The overall prevalence rates of general obesity and overweight classified by BMI were 15.0% (15.7% for men and 14.3% for women, p<0.01) and 19.2% (20.8% for men and 17.7% for women, p<0.01), respectively, and the overall prevalence rate of abdominal obesity was 37.6% (31.1% for men and women 43.9% for women, p<0.01). Multivariable logistic regression showed that the elderly and those who had a history of parental obesity, alcohol drinking, or former cigarette smoking were at high risk of obesity classified by BMI or WC, whereas those with a higher level of education, higher family income, or a healthy and balanced diet were at low risk of obesity. Analysis stratified by gender showed that men with a higher level education level, a white-collar job, a cadre job, or higher family income were the high risk group, and women with a higher level of education or higher family income were the low risk group.
Obesity and overweight have become epidemic in urban populations in China; associations of risk factors with obesity differ between men and women.
PMCID: PMC3509037  PMID: 23146089
General obesity; Abdominal obesity; Risk factors; Gender difference; Chinese urban adults
6.  Induction of KLF4 in response to heat stress 
Cell Stress & Chaperones  2006;11(4):379-389.
Krüppel-like factor 4 (KLF4) is an evolutionarily conserved zinc finger–containing transcription factor with diverse regulatory functions in cell growth, proliferation, differentiation, and embryogenesis. However, little is known about the response of KLF4 to heat stress. In this study, Western blot and reverse transcriptase–polymerase chain reaction were performed to determine the changes in KLF4 expression in response to heat stress. The results showed that heat stress up-regulated KLF4 messenger RNA and protein levels in a time-dependent manner in vivo and in 4 cell lines. Moreover, a study with heat shock transcription factor 1 (Hsf1) gene knockout mice indicated that the induction of KLF4 in response to heat stress was mediated by Hsf1. This process occurred rapidly, indicating that KLF4 is an immediate early response gene of heat stress. Next, the roles of KLF4 under heat stress conditions were analyzed for cells overexpressing or deficient in KLF4. The results showed overexpression of KLF4 increased the death rate of C2C12 cells, whereas KLF4 deficiency decreased the injury of C2C12 cells from heat stress conditions, suggesting that KLF4 might play an important role in cell injury induced by heat stress. KLF4 might be an immediate early response gene and could play an important role in cell injury induced by heat stress.
PMCID: PMC1712684  PMID: 17278886
7.  Viral Replication and Lung Lesions in BALB/c Mice Experimentally Inoculated with Avian Metapneumovirus Subgroup C Isolated from Chickens 
PLoS ONE  2014;9(3):e92136.
Avian metapneumovirus (aMPV) emerged as an important respiratory pathogen causing acute respiratory tract infection in avian species. Here we used a chicken aMPV subgroup C (aMPV/C) isolate to inoculate experimentally BALB/c mice and found that the aMPV/C can efficiently replicate and persist in the lungs of mice for at least 21 days with a peak viral load at day 6 postinoculation. Lung pathological changes were characterized by increased inflammatory cells. Immunochemical assay showed the presence of viral antigens in the lungs and significant upregulation of pulmonary inflammatory cytokines and chemokines including MCP-1, MIP-1α, RANTES, IL-1β, IFN-γ, and TNF-α were detected following inoculation. These results indicate for the first time that chicken aMPV/C may replicate in the lung of mice. Whether aMPV/C has potential as zoonotic pathogen, further investigation will be required.
PMCID: PMC3956885  PMID: 24637582
8.  Aspirin Promotes Oligodendrocyte Precursor Cell Proliferation and Differentiation after White Matter Lesion 
Cerebral white matter lesion (WML) is one of the main causes for cognitive impairment and is often caused by chronic cerebral hypoperfusion. A line of evidence has shown that aspirin has neuroprotective effects and produces some benefits in long-term outcome and survival for ischemic stroke patients. However, whether aspirin exerts a protective effect against WML is still largely unknown. Here, we showed that aspirin could promote oligodendrocyte precursor cell (OPC) proliferation and differentiation into oligodendrocytes after WML. Male Sprague-Dawley rats were subjected to permanent bilateral common carotid artery occlusion, a well-established model for WML. Four weeks later, Morris water maze test showed an impairment of learning and memory ability of rat while aspirin treatment improved behavioral performance. Low dose of aspirin (25 mg/kg) was found to elevate the number of OPCs while relatively high doses (100–200 mg/kg) increased that of oligodendrocytes, and ameliorated WML-induced the thinning of myelin, as revealed by the electron microscope. Similarly, our in vitro study also showed that relatively low and high doses of aspirin enhanced OPC proliferation and differentiation into oligodendrocytes, respectively. Furthermore, we revealed that aspirin enhanced extracellular signal-related kinase (ERK) but inhibited RhoA activities. In summary, we provided the first evidence that aspirin can promote oligodendrogenesis and oligodendrocyte myelination after WML, which may involve ERK and RhoA pathways.
PMCID: PMC3902474  PMID: 24478700
aspirin; oligodendrocytes; oligodendrocyte precursor cells; white matter lesion; extracellular signal-related kinase; RhoA
9.  Seoul Virus in Rats (Rattus norvegicus), Hyesan, North Korea, 2009–2011 
Emerging Infectious Diseases  2013;19(11):1895-1896.
PMCID: PMC3837658  PMID: 24229532
Seoul virus; Rattus norvegicus; Hyesan; North Korea; viruses; hantavirus
10.  Adsorption of Cu(II) on Oxidized Multi-Walled Carbon Nanotubes in the Presence of Hydroxylated and Carboxylated Fullerenes 
PLoS ONE  2013;8(8):e72475.
The adsorption of Cu(II) on oxidized multi-walled carbon nanotubes (oMWCNTs) as a function of contact time, pH, ionic strength, temperature, and hydroxylated fullerene (C60(OH)n) and carboxylated fullerene (C60(C(COOH)2)n) were studied under ambient conditions using batch techniques. The results showed that the adsorption of Cu(II) had rapidly reached equilibrium and the kinetic process was well described by a pseudo-second-order rate model. Cu(II) adsorption on oMWCNTs was dependent on pH but independent of ionic strength. Compared with the Freundlich model, the Langmuir model was more suitable for analyzing the adsorption isotherms. The thermodynamic parameters calculated from temperature-dependent adsorption isotherms suggested that Cu(II) adsorption on oMWCNTs was spontaneous and endothermic. The effect of C60(OH)n on Cu(II) adsorption of oMWCNTs was not significant at low C60(OH)n concentration, whereas a negative effect was observed at higher concentration. The adsorption of Cu(II) on oMWCNTs was enhanced with increasing pH values at pH < 5, but decreased at pH ≥ 5. The presence of C60(C(COOH)2)n inhibited the adsorption of Cu(II) onto oMWCNTs at pH 4–6. The double sorption site model was applied to simulate the adsorption isotherms of Cu(II) in the presence of C60(OH)n and fitted the experimental data well.
PMCID: PMC3756995  PMID: 24009683
11.  Avian Metapneumovirus Subgroup C Infection in Chickens, China 
Emerging Infectious Diseases  2013;19(7):1092-1094.
Avian metapneumovirus causes acute respiratory tract infection and reductions in egg production in various avian species. We isolated and characterized an increasingly prevalent avian metapneumovirus subgroup C strain from meat-type commercial chickens with severe respiratory signs in China. Culling of infected flocks could lead to economic consequences.
PMCID: PMC3903454  PMID: 23763901
Avian metapneumovirus subgroup C; Pneumovirinae; Paramyxoviridae; viruses; chickens; M gene sequencing; pathogenesis; China
12.  Development and Characterization of Simple Sequence Repeat Markers Providing Genome-Wide Coverage and High Resolution in Maize 
Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study.
PMCID: PMC3789560  PMID: 23804557
simple sequence repeat; whole-genome sequences; polymorphic SSR markers; teosinte; maize
13.  Complete Genome Sequence of Seoul Virus Isolated from Rattus norvegicus in the Democratic People's Republic of Korea 
Journal of Virology  2012;86(24):13853.
Seoul virus (SEOV) is responsible for 25% of cases of hemorrhagic fever with renal syndrome in Asia. Here we report the complete genome of strain DPRK08. The sequence information provided here is useful for understanding the molecular character of SEOV in the Democratic People's Republic of Korea (DPRK) and the circulation of SEOV in East Asia.
PMCID: PMC3503101  PMID: 23166256
14.  Predictive Equations Using Regression Analysis of Pulmonary Function for Healthy Children in Northeast China 
PLoS ONE  2013;8(5):e63875.
There have been few published studies on spirometric reference values for healthy children in China. We hypothesize that there would have been changes in lung function that would not have been precisely predicted by the existing spirometric reference equations. The objective of the study was to develop more accurate predictive equations for spirometric reference values for children aged 9 to 15 years in Northeast China.
Methodology/Principal Findings
Spirometric measurements were obtained from 3,922 children, including 1,974 boys and 1,948 girls, who were randomly selected from five cities of Liaoning province, Northeast China, using the ATS (American Thoracic Society) and ERS (European Respiratory Society) standards. The data was then randomly split into a training subset containing 2078 cases and a validation subset containing 1844 cases. Predictive equations used multiple linear regression techniques with three predictor variables: height, age and weight. Model goodness of fit was examined using the coefficient of determination or the R2 and adjusted R2. The predicted values were compared with those obtained from the existing spirometric reference equations. The results showed the prediction equations using linear regression analysis performed well for most spirometric parameters. Paired t-tests were used to compare the predicted values obtained from the developed and existing spirometric reference equations based on the validation subset. The t-test for males was not statistically significant (p>0.01). The predictive accuracy of the developed equations was higher than the existing equations and the predictive ability of the model was also validated.
We developed prediction equations using linear regression analysis of spirometric parameters for children aged 9–15 years in Northeast China. These equations represent the first attempt at predicting lung function for Chinese children following the ATS/ERS Task Force 2005 guidelines on spirometry standardization.
PMCID: PMC3646772  PMID: 23667682
15.  Association Study Confirmed Susceptibility Loci with Keloid in the Chinese Han Population 
PLoS ONE  2013;8(5):e62377.
Keloid is benign fibroproliferative dermal tumors with unknown etiology. Recently, a genome-wide association study (GWAS) in Japanese population has identified 3 susceptibility loci (rs873549 at 1q41, rs940187 and rs1511412 at 3q22.3, rs8032158 at 15p21.3) for keloid. In order to examine whether these susceptibility loci are associated with keloid in the Chinese Han population, twelve previously reported SNPs were selected for replication in 714 cases and 2,944 controls by using Sequenom MassArray system. We found three SNPs in two regions showed significant association with keloid in the Chinese Han population: 1q41 (rs873549, P = 3.03×10−33, OR = 2.05, 95% CI: 1.82–2.31 and rs1442440, P = 9.85×10−18, OR = 0.56, 95% CI: 0.49–0.64, respectively) and 15q21.3 (rs2271289 located in NEDD4, P = 1.02×10−11, OR = 0.66, 95% CI: 0.58–0.74). We also detected one risk haplotype AG (P = 1.36×10−31, OR = 2.02) and two protective haplotypes of GA and AA (GA, P = 1.94×10−19, OR = 0.53, AA, P = 0.00043, OR = 0.78, respectively) from the two SNPs (rs873549 and rs1442440). Our study confirmed two previously reported loci 1q41 and 15q21.3 for keloid in the Chinese Han population, which suggested the common genetic factor predisposing to the development of keloid shared by the Chinese Han and Japanese populations.
PMCID: PMC3646817  PMID: 23667473
16.  Electroacupuncture for Moderate and Severe Benign Prostatic Hyperplasia: A Randomized Controlled Trial 
PLoS ONE  2013;8(4):e59449.
To evaluate the effects of electroacupuncture (EA) on the International Prostate Symptom Score (IPSS), postvoid residual urine (PVR), and maximum urinary flow rate (Qmax), and explore the difference between EA at acupoints and non-acupoints in patients with moderate to severe benign prostate hyperplasia (BPH).
Subjects and Methods
Men with BPH and IPSS ≥8 were enrolled. Participants were randomly allocated to receive EA at acupoint (treatment group, n = 50) and EA at non-acupoint (control group, n = 50). The primary outcome measure includes the change of IPSS at the 6th week and the secondary outcome measures include changes of PVR and Qmax at the 6th week and change of IPSS at the 18th week.
100/192 patients were included. At the 6th week, treatment group patients had a 4.51 (p<0.001) and 4.12 (p<0.001) points greater decline in IPSS than the control group in the intention to treat (ITT) and per-protocol (PP) populations. At the 18th week, a 3.2 points (p = 0.001) greater decline was found in IPSS for the treatment. No significant differences were found between the two groups in Qmax at the 6th week (p = 0.819). No significant difference was observed in PVR (P = 0.35).
Acupoint EA at BL 33 had better effects on IPSS, but no difference on PVR and Qmax as compared with non-acupoint EA. The results indicate that EA is effective in improving patient's quality of life and acupoint may have better therapeutic effects than non-acupoints in acupuncture treatments of BPH.
Trial Registration NCT01218243.
PMCID: PMC3625218  PMID: 23593139
17.  Aurora-A Identifies Early Recurrence and Poor Prognosis and Promises a Potential Therapeutic Target in Triple Negative Breast Cancer 
PLoS ONE  2013;8(2):e56919.
Triple negative breast cancer (TNBC) acquires an unfavorable prognosis, emerging as a major challenge for the treatment of breast cancer. In the present study, 122 TNBC patients were subjected to analysis of Aurora-A (Aur-A) expression and survival prognosis. We found that Aur-A high expression was positively associated with initial clinical stage (P = 0.025), the proliferation marker Ki-67 (P = 0.001), and the recurrence rate of TNBC patients (P<0.001). In TNBC patients with Aur-A high expression, the risk of distant recurrence peaked at the first 3 years and declined rapidly thereafter, whereas patients with Aur-A low expression showed a relatively constant risk of recurrence during the entire follow-up period. Univariate and multivariate analysis showed that overexpression of Aur-A predicted poor overall survival (P = 0.002) and progression-free survival (P = 0.012) in TNBC. Furthermore, overexpression of Aur-A, associated with high Ki-67, predicted an inferior prognosis compared with low expression of both Aur-A and Ki-67. Importantly, we further found that Aur-A was overexpressed in TNBC cells, and inhibition of this kinase inhibited cell proliferation and prevented cell migration in TNBC. Our findings demonstrated that Aur-A was a potential therapeutic target for TNBC and inhibition of Aur-A kinase was a promising regimen for TNBC cancer therapy.
PMCID: PMC3577665  PMID: 23437271
18.  Comparison of modified percutaneous transhepatic variceal embolization and endoscopic cyanoacrylate injection for gastric variceal rebleeding 
AIM: To compare the efficacy of modified percutaneous transhepatic variceal embolization (PTVE) with 2-octyl-cyanoacrylate (2-OCA) and endoscopic variceal obturation (EVO) with an injection of 2-OCA for prophylaxis of gastric variceal rebleeding.
METHODS: In this retrospective study, the medical records of liver cirrhosis patients with gastric variceal bleeding who underwent either endoscopic 2-OCA (EVO) or modified PTVE using 2-OCA at Shandong Provincial Hospital from January 2006 to December 2008 were reviewed. Patient demographics, rebleeding rate, survival rate, and complications were compared between the two groups (PTVE and EVO). All results were expressed as mean ± SD, or as a percentage. Quantitative variables were compared by two sample Student t tests, and qualitative variables were compared by the Fisher exact test or the χ2 test (with Yates correction) where appropriate. A P value less than 0.05 was considered significant. Statistical computation was performed using SPSS 13.0 software.
RESULTS: A total of 77 patients were included; 45 patients who underwent EVO and 32 patients who received PTVE. During the follow-up (19.78 ± 7.70 mo in the EVO group, vs 21.53 ± 8.56 mo in the PTVE group) rebleeding occurred in 17 patients in the EVO group and in 4 patients in the PTVE group (37.78% vs 12.5%, P = 0.028). The cumulative rebleeding-free rate was 75%, 59%, and 49% in 1, 2, and 3 years respectively for EVO, and 93%, 84%, and 84% for PTVE (P = 0.011). Cox analysis was used to identify independent factors that predicted rebleeding after treatment. Variables including age, gender, cause, Child-Pugh classification, size of gastric varices (GV), location of GV, and treatment methods were analyzed. It was revealed that Child-Pugh classification [risk ratio (RR) 2.10, 95%CI: 1.03-4.28, P = 0.040], choice of treatment (RR 0.25, 95%CI: 0.08-0.80, P = 0.019), and size of GV (RR 2.14, 95%CI: 1.07-4.28, P = 0.032) were the independent factors for predicting rebleeding. Follow-up computed tomography revealed that cyanoacrylate was retained in the varices and in the feeding veins of PTVE patients. During the follow-up, eight patients in the EVO group and four patients in the PTVE group died. The cumulative survival rates at 1, 2, and 3 years were 93%, 84%, and 67% respectively in the EVO group, and 97%, 88%, and 74% respectively in the PTVE group. The survival rates were not significantly different between the two groups (P = 0.432). Cox analysis showed that the Child-Pugh classification was the most significant prognostic factor of survival (RR 2.77, 95%CI: 1.12-6.80, P = 0.027). The incidence of complications was similar in both groups.
CONCLUSION: With extensive and permanent obliteration of gastric varices and its feeding veins, PTVE with 2-OCA is superior to endoscopic 2-OCA injection for preventing gastric variceal rebleeding.
PMCID: PMC3574596  PMID: 23430149
Gastric varices; Endoscopic variceal obturation; Percutaneous transhepatic variceal embolization; 2-octyl-cyanoacrylate; Bleeding
20.  An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes 
PLoS ONE  2012;7(7):e40637.
Non-human primates have emerged as an important resource for the study of human disease and evolution. The characterization of genomic variation between and within non-human primate species could advance the development of genetically defined non-human primate disease models. However, non-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab-eating macaques and eight Japanese macaques. Over 91% of the target regions were captured in the non-human primate samples, although the specificity of the capture decreased as evolutionary divergence from humans increased. Both intra-specific and inter-specific DNA variants were identified; Sanger-based resequencing validated 85.4% of 41 randomly selected SNPs. Among the short indels identified, a majority (54.6%–77.3%) of the variants resulted in a change of 3 base pairs, consistent with expectations for a selection against frame shift mutations. Taken together, these findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.
PMCID: PMC3407233  PMID: 22848389
21.  Organization and Variation Analysis of 5S rDNA in Different Ploidy-level Hybrids of Red Crucian Carp × Topmouth Culter 
PLoS ONE  2012;7(6):e38976.
Through distant crossing, diploid, triploid and tetraploid hybrids of red crucian carp (Carassius auratus red var., RCC♀, Cyprininae, 2n = 100) × topmouth culter (Erythroculter ilishaeformis Bleeker, TC♂, Cultrinae, 2n = 48) were successfully produced. Diploid hybrids possessed 74 chromosomes with one set from RCC and one set from TC; triploid hybrids harbored 124 chromosomes with two sets from RCC and one set from TC; tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from TC. The 5S rDNA of the three different ploidy-level hybrids and their parents were sequenced and analyzed. There were three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) in RCC and two monomeric 5S rDNA classes (designated class IV: 188 bp, and class V: 286 bp) in TC. In the hybrid offspring, diploid hybrids inherited three 5S rDNA classes from their female parent (RCC) and only class IV from their male parent (TC). Triploid hybrids inherited class II and class III from their female parent (RCC) and class IV from their male parent (TC). Tetraploid hybrids gained class II and class III from their female parent (RCC), and generated a new 5S rDNA sequence (designated class I–N). The specific paternal 5S rDNA sequence of class V was not found in the hybrid offspring. Sequence analysis of 5S rDNA revealed the influence of hybridization and polyploidization on the organization and variation of 5S rDNA in fish. This is the first report on the coexistence in vertebrates of viable diploid, triploid and tetraploid hybrids produced by crossing parents with different chromosome numbers, and these new hybrids are novel specimens for studying the genomic variation in the first generation of interspecific hybrids, which has significance for evolution and fish genetics.
PMCID: PMC3377697  PMID: 22720007
22.  Cloning and Functional Analysis of FLJ20420: A Novel Transcription Factor for the BAG-1 Promoter 
PLoS ONE  2012;7(5):e34832.
BAG-1 is an anti-apoptotic protein that interacts with a variety of cellular molecules to inhibit apoptosis. The mechanisms by which BAG-1 interacts with other proteins to inhibit apoptosis have been extensively explored. However, it is currently unknown how BAG-1 expression is regulated at the molecular level, especially in cancer cells. Here we reported to clone a novel down-regulated BAG-1 expression gene named FLJ20420 using hBAG-1 promoter as a probe to screen Human Hela 5′ cDNA library by Southernwestern blot. The FLJ20420 gene encodes a ∼26-kDa protein that is localized in both the cytoplasm and nucleus. We proved that FLJ20420 protein can specially bind hBAG-1 promoter region by EMSA in vivo and ChIP assay in vivo. Northern blot analysis revealed a low level of FLJ20420 transcriptional expression in normal human tissues (i.e., brain, placenta, lung, liver, kidney, pancreas and cervix), except for heart and skeletal muscles, which showed higher levels. Furthermore, enhanced FLJ20420 expression was observed in tumor cell lines (i.e., MDA468, BT-20, MCF-7, C33A, HeLa and Caski). Knockdown of endogenous FLJ20420 expression significantly increased BAG-1 expression in A549 and L9981 cells, and also significantly enhanced their sensitivity to cisplatin-induced apoptosis. A microarray assay of the FLJ20420 siRNA –transfectants showed altered expression of 505 known genes, including 272 upregulated and 233 downregulated genes. Finally, our gene array studies in lung cancer tissue samples revealed a significant increase in FLJ20420 expression in primary lung cancer relative to the paired normal lung tissue controls (p = 0.0006). The increased expression of FLJ20420 corresponded to a significant decrease in BAG-1 protein expression in the primary lung cancers, relative to the paired normal lung tissue controls (p = 0.0001). Taken together, our experiments suggest that FLJ20420 functions as a down-regulator of BAG-1 expression. Its abnormal expression may be involved in the oncogenesis of human malignancies such as lung cancer.
PMCID: PMC3342300  PMID: 22567091
23.  MiR-128 Inhibits Tumor Growth and Angiogenesis by Targeting p70S6K1 
PLoS ONE  2012;7(3):e32709.
MicroRNAs are a class of small noncoding RNAs that function as critical gene regulators through targeting mRNAs for translational repression or degradation. In this study, we showed that miR-128 expression levels were decreased in glioma, and identified p70S6K1 as a novel direct target of miR-128. Overexpression of miR-128 suppressed p70S6K1 and its downstream signaling molecules such as HIF-1 and VEGF expression, and attenuated cell proliferation, tumor growth and angiogenesis. Forced expression of p70S6K1 can partly rescue the inhibitory effect of miR-128 in the cells. Taken together, these findings will shed light to the role and mechanism of miR-128 in regulating glioma tumor angiogenesis via miR-128/p70S6K1 axis, and miR-128 may serve as a potential therapeutic target in glioma in the future.
PMCID: PMC3307714  PMID: 22442669
24.  Draft Genome Sequence of Gordonia neofelifaecis NRRL B-59395, a Cholesterol-Degrading Actinomycete▿ 
Journal of Bacteriology  2011;193(18):5045-5046.
We report a draft sequence of the genome of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete isolated from fresh feces of a clouded leopard (Neofelis nebulosa). As predicted, the reported genome contains several gene clusters for cholesterol degradation. This is the second available genome sequence of the family Gordoniaceae.
PMCID: PMC3165644  PMID: 21742880
25.  Associations of HLA-DP Variants with Hepatitis B Virus Infection in Southern and Northern Han Chinese Populations: A Multicenter Case-Control Study 
PLoS ONE  2011;6(8):e24221.
Human leukocyte antigen DP (HLA-DP) locus has been reported to be associated with hepatitis B virus (HBV) infection in populations of Japan and Thailand. We aimed to examine whether the association can be replicated in Han Chinese populations.
Methodology/Principal Findings
Two HLA-DP variants rs2395309 and rs9277535 (the most strongly associated SNPs from each HLA-DP locus) were genotyped in three independent Han cohorts consisting of 2 805 cases and 1 796 controls. By using logistic regression analysis, these two SNPs in the HLA-DPA1 and HLA-DPB1 genes were significantly associated with HBV infection in Han Chinese populations (P = 0.021∼3.36×10−8 at rs2395309; P = 8.37×10−3∼2.68×10−10 at rs9277535). In addition, the genotype distributions of both sites (rs2395309 and rs9277535) were clearly different between southern and northern Chinese population (P = 8.95×10−5 at rs2395309; P = 1.64×10−9 at rs9277535). By using asymptomatic HBV carrier as control group, our study showed that there were no associations of two HLA-DP variants with HBV progression (P = 0.305∼0.822 and 0.163∼0.881 in southern Chinese population, respectively; P = 0.097∼0.697 and 0.198∼0.615 in northern Chinese population, respectively).
Our results confirmed that two SNPs (rs2395309 and rs9277535) in the HLA-DP loci were strongly associated with HBV infection in southern and northern Han Chinese populations, but not with HBV progression.
PMCID: PMC3164164  PMID: 21904616

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