[Show abstract][Hide abstract] ABSTRACT: Haplogroup N-M231 of human Y chromosome is a common clade from Eastern Asia
to Northern Europe, being one of the most frequent haplogroups in Altaic and
Uralic-speaking populations. Using newly discovered bi-allelic markers from
high-throughput DNA sequencing, we largely improved the phylogeny of Haplogroup
N, in which 16 subclades could be identified by 33 SNPs. More than 400 males
belonging to Haplogroup N in 34 populations in China were successfully
genotyped, and populations in Northern Asia and Eastern Europe were also
compared together. We found that all the N samples were typed as inside either
clade N1-F1206 (including former N1a-M128, N1b-P43 and N1c-M46 clades), most of
which were found in Altaic, Uralic, Russian and Chinese-speaking populations,
or N2-F2930, common in Tibeto-Burman and Chinese-speaking populations. Our
detailed results suggest that Haplogroup N developed in the region of China
since the final stage of late Paleolithic Era.
[Show abstract][Hide abstract] ABSTRACT: By using the Fourier transform infrared spectroscopy and linear discriminant analysis (LDA), logistic discriminant analysis (Logistic-DA), principal component analysis-linear discriminant analysis (PCA-LDA), partial least-squares discriminant analysis (PLS-DA), random forest (RF), support vector machine (SVM), infrared spectra of 60 kinds of plant extract of Chinese traditional medicine were analyzed and the identification and evaluation of characteristics of the regional markers associated with cold and heat nature were studied. Results indicated that LDA and SVM are suitable for the recognition model of water extract infrared spectral data, LDA is suitable for the identification model of anhydrous ethanol extract infrared spectral data, SVM is suitable for the identification model of chloroform extract infrared spectral data, while petroleum ether extract group recognition effect is not ideal. According to the suitable characteristic parameters identification model, data were analyzed by infrared spectroscopy, and parameters and resistance characteristics of the traditional Chinese drug composition can be obtained. Regional characteristics of these two parameters can be used to identify drug ingredients, and can also be used to indicate different degrees of resistance characteristics of traditional Chinese medicine. Component parameter is model identification coefficient corresponding to the position of spectrum and infrared, with a value greater than zero it is cold nature marker, while with a value less than zero it is heat nature marker; model identification score is a parameter reflecting the degree of cold and heat nature, the greater the score (positive), the more it is cold, while the smaller the score, the more it is hot. a parameter reflecting the degree of cold and heat,the greater the score (positive) is cold more strong, the score is small (negative) heat stronger.
No preview · Article · May 2014 · Guang pu xue yu guang pu fen xi = Guang pu
[Show abstract][Hide abstract] ABSTRACT: To establish signature pattern recognition model of cold-hot nature of herbal medicine.
High performance capillary electrophoresis fingerprints of 60 kinds of herbal medicine (30 kinds of cold, 30 of hot) were established, features of wavelength were screened, 6 analysis methods such as linear discriminant analysis (LDA), logistic discriminant analysis (Logistic-DA), principal component and linear discriminant analysis (PCA-LDA), partial least-squares discriminant analysis (PLS-DA), random forest (RF) and support vector machine (SVM) were used to establish and evaluate recognition model of cold-hot nature after data processing.
SVM was proved to be a suitable means of recognition model of herbal medicine cold-hot nature based on data of HPCE fingerprints. Characteristic parameters of nature could be screened according to theoretical spectra signature of nature model, the characteristic regions of components of herbs with cold-heat nature could be identified in the HPCE fingerprint. The characteristic parameters of cold-hot nature were the identifying coefficient for specific retention time of the theoretical spectra of recognition model, identification coefficients greater than zero were for the cold marker, while that less than zero for the hot marker.
The results imply that HPCE is a feasible and effective means for identification of cold-hot nature of Traditional Chinese medicine.
No preview · Article · Sep 2013 · Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials
[Show abstract][Hide abstract] ABSTRACT: To investigate the genetic polymorphisms of 15 X-STR loci in Shandong Han population in order to establish the forensic application database.
The multi-PCR primers of these loci were designed by Primer Premier 5.0 software and labeled by 4 fluoresceins (FAM, VIC, NED and TET). The developed multi-PCR was used to investigate 15 X-STR loci (DXS10011, DXS101, GATA 165B12, DXS6795, DXS6800, DXS6801, DXS6803, DXS7132, DXS7133, DXS7423, DXS7424, DXS8377, DXS8378, DXS9898 and HPRTB) selected from the X chromosome of 481 unrelated individuals (295 females and 186 males) in Shandong Han population.
Among the 15 X-STR loci, GATA 165B12, DXS6800, DXS6803, DXS7133 and DXS7423 showed moderate polymorphisms, while the rest 10 X-STR loci showed high polymorphisms (PIC > 0.5 and H > 0.5). No shared haplotype was detected among the males in Shandong Han population.
The developed multi-PCR system with fluorescence detection provides an effective way to establish X-STR loci database of population genetics in Shandong Han population and shows its forensic application.
No preview · Article · Jun 2013 · Fa yi xue za zhi
[Show abstract][Hide abstract] ABSTRACT: To evaluate the relationship between lifestyle habits and the components of metabolic syndrome (MS).
Based on the routine health check-up system in a certain Center for Health Management of Shandong Province, a longitudinal surveillance health check-up cohort from 2005 to 2010 was set up. There were 13 225 urban workers in Jinan included in the analysis. The content of the survey included demographic information, medical history, lifestyle habits, body mass index (BMI) and the level of blood pressure, fasting blood-glucose, and blood lipid, etc. The distribution of BMI, blood pressure, fasting blood-glucose, blood lipid and lifestyle habits between MS patients and non-MS population was compared, latent variables were extracted by exploratory factor analysis to determine the structure model, and then a partial least squares path model was constructed between lifestyle habits and the components of MS.
Participants'age was (46.62 ± 12.16) years old. The overall prevalence of the MS was 22.43% (2967/13 225), 26.49% (2535/9570) in males and 11.82% (432/3655) in females. The prevalence of the MS was statistically different between males and females (χ(2) = 327.08, P < 0.01). Between MS patients and non-MS population, the difference of dietary habits was statistically significant (χ(2) = 166.31, P < 0.01) in MS patients, the rate of vegetarian, mixed and animal food was 23.39% (694/2967), 42.50% (1261/2967) and 34.11% (1012/2967) respectively, while in non-MS population was 30.80% (3159/10 258), 46.37% (4757/10 258), 22.83% (2342/10 258) respectively. Their alcohol consumption has statistical difference (χ(2) = 374.22, P < 0.01) in MS patients, the rate of never or past, occasional and regular drinking was 27.37% (812/2967), 24.71% (733/2967), 47.93% (1422/2967) respectively, and in non-MS population was 39.60% (4062/10 258), 31.36% (3217/10 258), 29.04% (2979/10 258) respectively. The difference of their smoking status was statistically significant (χ(2) = 115.86, P < 0.01) in MS patients, the rate of never or past, occasional and regular smoking was 59.72% (1772/2967), 6.24% (185/2967), 34.04% (1010/2967) respectively, while in non-MS population was 70.03% (7184/10 258), 5.35% (549/10 258), 24.61% (2525/10 258) respectively. Both lifestyle habits and the components of MS were attributable to only one latent variable. After adjustment for age and gender, the path coefficient between the latent component of lifestyle habits and the latent component of MS was 0.22 with statistical significance (t = 6.46, P < 0.01) through bootstrap test. Reliability and validity of the model:the lifestyle latent variable: average variance extracted was 0.53, composite reliability was 0.77 and Cronbach's a was 0.57. The MS latent variable: average variance extracted was 0.45, composite reliability was 0.76 and Cronbach's a was 0.59.
Unhealthy lifestyle habits are closely related to MS. Meat diet, excessive drinking and smoking are risk factors for MS.
No preview · Article · Apr 2013 · Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]
[Show abstract][Hide abstract] ABSTRACT: Human cytomegalovirus (HCMV) infection is a major cause of morbidity in the recipients of organ transplants and in the congenitally infected infants. HCMV vaccine has emerged as an effective approach to prevent HCMV infection particularly for the development of multiple viral antigens vaccination and human leukocyte antigen (HLA)-restricted polyepitope technology. As the Chinese population makes up more than one fifth of the population worldwide, it is important to develop HCMV vaccines more specific for the Chinese population by targeting Chinese-restricted HLA alleles and antigens. In the present study, we designed a novel chimeric polyepitope vaccine based on the replication-deficient adenovirus Ad5F35, which encodes 83 HCMV T cell epitopes from 15 different HCMV antigens, restricted to 14 HLA I and 7 HLA II alleles that cover 92% of the Chinese population. Our results show that the recombinant adenovirus vaccine Ad5F35-CTL·Th can be efficiently transfected and expressed in peripheral blood mononuclear cells (PBMCs) with little cytopathic activity. Ad5F35-CTL·Th can also be endogenously processed and presented by PBMCs. Ad5F35-CTL·Th-stimulated HCMV-specific cytotoxic T lymphocytes (CTLs) showed strong cytolytic activity against HCMV polyepitope-sensitized target cells. The CTL activity was accompanied by high levels of IFN-γ production after Ad5F35-CTL·Th stimulation. The specificity and vigorous response to the recombinant adenovirus vaccine in vitro makes it a potential candidate to be used for transplantation recipients or congenitally infected infants.
No preview · Article · Dec 2011 · Antiviral research
[Show abstract][Hide abstract] ABSTRACT: Hemorrhagic fever with renal syndrome (HFRS) is endemic in Junan county, Shandong Province, China. We conducted geographic information system (GIS)-based spatial analysis with the objective of estimating the spatial distribution of rodent populations and their hantavirus infection patterns, to describe the spatial relationships of hantavirus strains in small ecological areas and to identify key areas in endemic areas of HFRS for future public health planning and resource allocation.
Rodent sampling was conducted in seven villages in Junan county from February 2006 to January 2007 using field epidemiological surveillance. Dynamics of hantavirus infection and population densities in rodents were investigated. Spatial statistical techniques including Ripley' L index and nearest neighbour hierarchical (NNH) clustering analysis were conducted to reveal the spatial structure of rodent populations in seven villages. Phylogenetic analysis and two-dimensional minimal spanning tree (2-D MST) models were employed to describe the spatial relationship of hantavirus strains.
Data showed that Mus musculus was the most common species in our study area, followed by Rattus norvegicus. Ripley's L index and NNH analysis showed that the spatial distribution of all captured rodents, Mus musculus and Rattus norvegicus in seven villages were clustered and there were hotspot areas of rodent distribution. The branches of 2-D MSTs had similar topologies to those of corresponding phylogenetic trees, and hantavirus strains exhibited obvious connective traces in seven villages.
These results contribute to the understanding of the spatial distribution of rodent populations and hantavirus infection patterns in small areas, and identify priority areas within the epidemic areas for the development of a better prevention strategy against hemorrhagic fever with renal syndrome in a small ecological area.
No preview · Article · Jun 2011 · Chinese medical journal
[Show abstract][Hide abstract] ABSTRACT: Previous studies suggest that TNFSF4 is a susceptibility gene of atherosclerosis. But case-control association analysis in Swedish population and German population provided inconsistent, even opposite results. In order to explore the relationship between this gene and coronary heart disease (CHD) in Chinese Han population, we collected 498 cases and 509 controls from Qilu hospital of Shandong University and analyzed the association between five single-nucleotide polymorphisms (SNPs) (rs1234314, rs45454293, rs3850641, rs1234313, and rs3861950) of TNFSF4 and CHD. On the basis of using traditional statistical analysis methods based on single SNP and haplotypes, we introduced principal component score-based logistic regression analysis to deal with the data. The results suggested that in Armitage trend test, only rs3861950 was significant, when used the Bonferroni correction, and all of the five SNPs were not statistically significant. In the logistic regression analysis which adjusts the confounding factors, all of the five SNPs were not statistically significant. In haplotype analysis, the frequencies of six haplotypes were significantly different in cases and controls (CTAGT (P=0.0006), CTAAC (P=0.0123), CCAGT (P=0.0004), GTGGT (P=0.0329), GCGAC (P<0.0001), and GCAAC (P=0.0173)). In principal component score-based logistic regression analysis, the first principal component has statistical significance (P=0.0236). These results indicate that TNFSF4 is a susceptibility gene of CHD in Chinese Han population.
No preview · Article · Mar 2011 · Hereditas (Beijing)
[Show abstract][Hide abstract] ABSTRACT: To study the incidence and spatiotemporal dynamic variation of hemorrhagic fever with renal syndrome (HFRS) in Shandong province.
According to surveillance data on HFRS epidemics and host animals, a 'contour area multifractal model' was estimated on the HFRS' incidence and multi-analysis model was applied to study spatiotemporal dynamic variation.
The process could be classified into 5 periods: 1st period (1974-1981) when HFRS was in completely natural focal state in Shandong, and the nature of focus was typical Apodemus type. 2nd period (1982-1986) indicated the process of expanding and merging of the Apodemus type focus in the southeastern part of Linyi district and the Rattus type focus was in the southern part of Jining city. 3rd period (1987-1990) indicated that through the expanding and merging of the two epidemic focuses,one mixed focus dominated by the Apodemus type had been formed in the hilly area of the southern and middle part of Shandong while another one dominated by the Rattus type in the Yellow River valley of the northwestern part of Shandong. 4th period (1991-1993) showed that the process of the spatial pattern of the mixed focus dominated by the Rattus type in Shandong. 5th period (1994-2004) referred to the spatial pattern of the mixed focus dominated by the Rattus became stabilized.
Evolution of the characteristics of HFRS focus in Shandong province experienced the following three processes: the simple Apodemus type and the simple Rattus type were seen separately to the mixed foci with the Apodemus type dominant and the Rattus dominant type coexisted and merged to the stable state of the mixed focus with Rattus as the dominant one.
No preview · Article · Jun 2007 · Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi
[Show abstract][Hide abstract] ABSTRACT: At present study, the reasons of "horse-shoe effect" in correspondence analysis for analyzing human population genetic structure was explained. Based on the structure of gene frequency matrix, we displaye the different patterns of Scallergram of correspondent analysis from different types of loci (HLA-A locus, and STR- CSF1PO locus in Chinese Han populations). The results indicate that different types of loci showed different patterns of Scallergram of correspondent analysis. When some alleles have very low frequency in the gene frequency matrix, there would be "horse-shoe effect" in the Scallergram of correspondent analysis. The reason is that the c2 distance measurement in correspondent analysis usually overrates the effect of the genes with low frequencies. To carry out the correspondent analysis of human population genetic structure, when the Scallergram presents "horse-shoe effect", one should examine the structure of gene frequency matrix, and confirm whether the "horse-shoe effect" shows the real pattern of population genetic structure. Only in this way, one can explain the "horse-shoe effect" correctly.
No preview · Article · Dec 2005 · Hereditas (Beijing)
[Show abstract][Hide abstract] ABSTRACT: To explore the spatial genetic structure of two HIV-I-resistant polymorphisms (CCR2-64 I and SDF1-3'A) alleles in the population of Shandong Province, China.
Using the techniques of spatial stratified sampling and spatial statistics, the spatial genetic structure of the locus (CCR2-64 I and SDF1-3'A), which was shown to be important co-receptor for HIV infection, was quantified from the populations of 36 sampled counties of Shandong Province, and a total of 3147 and 3172 samples were taken for testing CCR2-64I and SDF1-3'A respectively from individuals without known history of HIV-I infection and AIDS symptoms.
There were significantly spatial genetic structures of the two alleles at different spatial distance classes on the scale of populations, but on the scale of individuals, no spatial structure was found in either the whole area of Shandong Province or the area of each sampled county. Although the change of frequencies of the two alleles with geographic locations in Shandong Province both showed gradual increase trends, their changing directions were inverse. The frequency of CCR2-64I allele gradually increased from the southwest to the northeast, while the frequency of SDF1-3'A allele gradually increased from the northeast to the southwest. However the RH to AIDS of combined types of their different genotypes did not represent obvious geographic diversity on the whole area of the Province.
The frequency of allele usually has some spatial genetic structures or spatial autocorrelation with different spatial distance classes, but the genotypes of individuals have random distribution in the same geographic area. Evaluating spatial distribution of the genetic susceptibility of HIV (AIDS) to CCR2-64I and SDF1-3'A alleles, should focus on the frequencies of combined genotypes of CCR2 and SDF1 based on the two-locus genotypes of each individual rather than the frequencies of CCR2-64I and SDF1-3'A alleles.
No preview · Article · Sep 2005 · Biomedical and Environmental Sciences
[Show abstract][Hide abstract] ABSTRACT: This paper presents the application of Kriging technique in the field of human population genetics for quantifying the spatial genetic heterogeneity of HLA-A locus in the area of China,and for mapping its spatial genetic structure using the measurement of synthetic genetic structure (SPC) and the principal components (PC). Both principles of the method and the basic equations are given. The Kriging model has several advantages over other interpolation and smoothing methods. Firstly, it relies on the structure of the spatial genetic semivariogram model, which can be used to quantify the spatial genetic heterogeneity of the locus (loci) before mapping its spatial genetic structure. Secondly, it is virtually unbiased in the interpolation situation,where the location to be estimated is surrounded by data on all sides and is influenced within the range of these data. Thirdly, it allows of estimative error of interpolation, which can be used to appraise the predicting effect for the spatial estimation,and the error maps can be used to decide where to introduce new sampling population genetic data. However, the "Kriging" model also has some disadvantages. Firstly,when the theoretical spatial genetic semivariogram can not be fitted by any models, the "Kriging" model can not be set up. Secondly, if the Kriging model was built by a poor spatial genetic semivariogram,the Kriging estimation standard deviation is remarkably high in the whole area, hence the Kriging model can not be suitable to estimating the distribution of spatial genetic structure. In these situations,the interpolation algorithm, whose assumption is spatial random rather than spatial autocorrelation,such as the Cavalli-Sforza method in Genography, inverse distance-weighted methods, splines, should be used to estimate or map the distribution of spatial genetic structure.
[Show abstract][Hide abstract] ABSTRACT: The distribution and structure of the allelic polymorphism data are analyzed and it is pointed out that the distribution of allelic polymorphism data reveals the characteristic of closed data (also named as compositional data or data of constant sum). It is interpreted that the correlation structure of the allelic polymorphism data contains null correlations introduced by "closure" and the statistical distribution of the data is not normal because of its constant row sum, which resulted in great difficulties in analyzing the data with traditional multiple linear statistical methods such as principal component analysis, factor analysis, cluster analysis and canonical correlation analysis. Based on the theory of compositional data analysis proposed by Aitchison in 1982, a multiple nonlinear statistical method originating from the "logratios" approach to the statistical analysis of compositional data is put forward in this paper. As an example, the "logratios" method was used to analyze the genetic structure of TH01 polymorphic loci in Chinese population and the results were compared with those of multiple linear methods such as component principal. It is concluded that the "logratios" multiple nonlinear principle component analysis is a better method with the virtue of sensitivity and specificity for analyzing the genetic structure of population from the data of allelic polymorphism.
Preview · Article · Mar 2004 · Acta Genetica Sinica