Obvious epigenetic differentiation occurred on Lycium barbarum in different cultivation areas in China. To investigate the difference and change rule of DNA methylation level and pattern of L. barbarum from different cultivation areas in China, the present study employed fluorescence-assisted methylation-sensitive amplified polymorphism(MSAP) to analyze the methylation level and polymorphism of 53 genomic DNA samples from Yinchuan Plain in Ningxia, Bayannur city in Inner Mongolia, Jingyuan county and Yumen city in Gansu, Delingha city in Qinghai, and Jinghe county in Xinjiang. The MSAP technical system suitable for the methylation analysis of L. barbarum genomic DNA was established and ten pairs of selective primers were selected. Among amplified 5'-CCGG-3' methylated sites, there were 35.85% full-methylated sites and 39.88% hemi-methylated sites, showing a high degree of epigenetic differentiation. Stoichiometric analysis showed that the ecological environment was the main factor affecting the epigenetic characteristics of L. barbarum, followed by cultivated varieties. Precipitation, air temperature, and soil pH were the main ecological factors affecting DNA methylation in different areas. This study provided a theoretical basis for the analysis of the epigenetic mechanism of L. barbarum to adapt to the diffe-rent ecological environments and research ideas for the introduction, cultivation, and germplasm traceability of L. barbarum.
China ; DNA Methylation ; DNA Primers ; Epigenesis, Genetic ; Lycium/genetics*

The important role of intestinal microorganisms in human health has been widely confirmed. At present, most of the studies on intestinal microorganisms are based on amplification of the V3-V4 region of bacterial 16S rRNA gene, and little attention has been paid to archaea. In this study, a primer set which can amplify 16S rRNA gene of both bacteria and archaea at the same time was used. By comparing the community changes before and after probiotics intake, it showed that this primer set is suitable for analyzing the changes of human intestinal bacteria and archaea communities. The fecal samples of volunteers were collected, and the amplification and high-throughput sequencing were carried out by using bacterial primer set (B primer) and bacterial and archaeal universal primer (AB primer); several commonly used rRNA databases were used to determine the amplification ability of the primer set to bacteria and archaea. The results showed that AB primer could display the bacterial community amplified by B primer, and could obtain the sequence of common methanogenic archaea in intestinal tract. AB primer set can analyze the bacteria and archaea in the intestinal tract at the same time by only one amplification and sequencing, which can show the structure of intestinal microbial community more comprehensively, which is suitable for the research of intestinal microorganisms.
Archaea/genetics* ; Bacteria/genetics* ; DNA Primers ; DNA, Bacterial ; Humans ; Microbiota/genetics* ; Phylogeny ; RNA, Ribosomal, 16S/genetics*

To investigate the genetic diversity among wild Dipsacus asperoides in China, 66 germplasmic resources of D. asperoides were analyzed by Start Codon Targeted Polymorphism (SCoT) molecular markers. Genetic distance was calculated by TREECONW software and the systematic diagram of genetic relationship was clustered by UPGMA method. The results showed that the totals of 181 bands were detected using 20 primers , among which 109 were polymorphic bands. The average percentage of polymorphic bands was 60.13%. Genetic distance changed from 0.030 6 to 0.181 4. The clustering results showed that there was no significant correlation between the classification of the wild D. asperoides and their geographical origin. The relatively high genetic diversity of D. asperoides provides the basis for breeding new varieties.
China ; DNA Primers ; genetics ; DNA, Plant ; genetics ; Dipsacaceae ; chemistry ; classification ; genetics ; Genetic Variation ; Phylogeny ; Polymorphism, Genetic

OBJECTIVETo study the identification method of Syngnathus and its adulterants.

METHODRandom amplified polymorphic DNA (RAPD) was used to construct a dendrogram by UPGMA method based on Nei & Li's coefficient and a genetic affinity pattern for Syngnathus acus, Solenognathus hardwickii, Syngnathoides biaculeatus, Trachyrhamphus serratus, Halicampus koilomatodon, Microphis boaja.

RESULTFour primers, LJ04, LJ09, LJ16 and LJ19, from 18 random primers were used in the dendrogram which can differentiate Syngnathus in genus level and showed a great consistence with the appearance identification. The genetic affinity pattern based on primers LJ09 and LJ19 could be used to identify Syngnathus from its adulterants.

CONCLUSIONRAPD is suitable to identify Syngnathus and its adulterants.

Animals ; China ; DNA Primers ; genetics ; Phylogeny ; Polymorphism, Genetic ; Random Amplified Polymorphic DNA Technique ; Smegmamorpha ; classification ; genetics

To evaluate the roles of 8 short tandem repeats (STR) loci as STR panel in quantitative analysis of chimerism following transplantation, the primers were synthesized and marked with different dyes for D3S3045, D4S2366, D4S2639, D5S818, D13S317, D18S1002, D20S481 and D22S689. The blood samples of 15 cases received allogeneic stem cell transplantation were collected before and after transplantation, then DNA was extracted and amplified with these primers, and was further analysed under ABI Genetic Analyser 3100 to select suitable informative STR locus. Donor/recipient dilution series were prepared to get standard curves in selected loci, the DNAs extracted at different days after transplantation were used to quantitatively analyze the chimerism in patients according to the values of peak area or peak height of fluorescent signals. The standard curves can be used to calculate the chimerism by plotting the respective R/D quotient value against the percentage of recipient DNA. The results indicated that the calculated chimerism was in concordance with the donor/recipient dilution. The STR panel succeeded in identifying at least one informative marker and quantitative monitoring the chimerism after HSCT in 15 donor-recipient pairs and a relapsed case was diagnosed. It is concluded that the STR panel and its detection method can accurately and quantitatively monitor the chimerism after allogeneic HSCT, which is more economical and flexible than using commercial kits.
DNA ; genetics ; DNA Primers ; Hematopoietic Stem Cell Transplantation ; Humans ; Microsatellite Repeats ; Transplantation Chimera ; genetics

OBJECTIVE: To explore the change rules of peak area ratio of STR loci to Amelogenin (AMEL) locus (STR/AMEL), a sex-determining gene in DNA degradation, and to evaluate the application of STR/AMEL value in the estimation of DNA degradation degree. METHODS: DNA was extracted from iliopsoas, and the variations of STR/AMEL value (Penta E/AMEL, Penta D/AMEL, FGA/AMEL) were analyzed after the artificial degradation was made by DNase I, and the changes of these three ratios of the iliopsoas naturally degraded in an outdoor environment were also analyzed. The regression curves were analyzed using the periods of DNA degradation and outside the body as the independent variable (x) and the STR/AMEL value as the dependent variable (y) and three curve equations under two conditions were established. RESULTS: Both under the conditions of artificial and natural degradation, STR/AMEL value had a negative relationship with the degradation time. The relationship between STR/AMEL and degradation time can be well simulated by the cubic function. R2 was over 0.99 under controlled degradation condition and over 0.86 under natural degradation condition. CONCLUSION The STR/AMEL value (Penta E/AMEL, Penta D/AMEL, FGA/AMEL) is negatively related with the DNA degradation degree, which follows mathematical regression models strictly, and it might be applied to evaluate the DNA degradation degree.
Amelogenin/genetics* ; DNA Damage/genetics* ; DNA Primers ; Humans ; Microsatellite Repeats ; Regression Analysis ; Time Factors

Genetic diversity of Lilium sargentiae was detected in this paper by sequence-related amplified polymorphism (SRAP) marker. One hundred wild samples were collected from 10 places, and 15 SRAP primer combinations were used for determination. NTSYS-pc2.1 and POPGEN1.32 were used for data analysis. The results showed that a total of 170 clear DNA bands were amplified, 163 of which were polymorphic. The proportion of polymorphic loci was 90.58% on the level of species. Nei's (1973) gene diversity (H) was 0.2631, Shannon's Information index was 0.3661, the G(st), was 0.3672, and the genetic distance ranged from 0.2021 to 0.5749. All materials could be clustered into four groups by UPGMA. The results demonstrated that the genetic diversity of L. sargentiae was rich on the level of species, and the genetic diversity within populations exceeded among populations. The correlations of genetic diversity and distribution were significant in L. sargentiae.
Cluster Analysis ; Conservation of Natural Resources ; DNA Primers ; genetics ; Genetic Markers ; genetics ; Lilium ; genetics ; Polymorphism, Genetic ; genetics

OBJECTIVETo design specific primers and authenticate Atractylodes macrocephala from Atractylodes lancea and A. chinensis.

METHODSNPs in the psbA-trnH sequences of Atractylodes were found by ClustulW program and Bioedit software. Primers for authentic A. macrocephala is designed according to the SNP site, and ITS sequence universal primers plus to the authentic primer to construct a multi-PCR reaction system, and then optimized the PCR reaction system.

RESULT172 bp band special for A. macrocephala were found using multi-PCR reaction.

CONCLUSIONThe multi-PCR reaction system could be applied to identify A. macrocephala seed.

Atractylodes ; genetics ; DNA Primers ; genetics ; Mutation ; Polymerase Chain Reaction ; methods ; Quality Control ; Seeds ; genetics

To obtained an accurate, rapid and efficient method for authenticate medicinal snakes listed in Chinese Pharmacopoeia (Zaocysd humnades, Bungarus multicinctus, Agkistrodon acutus), a rapid PCR method for authenticate snakes and its adulterants was established based on the classic molecular authentication methods. DNA was extracted by alkaline lysis and the specific primers were amplified by two-steps PCR amplification method. The denatured and annealing temperature and cycle numbers were optimized. When 100 x SYBR Green I was added in the PCR product, strong green fluorescence was visualized under 365 nm UV whereas adulterants without. The whole process can complete in 30-45 minutes. The established method provides the technical support for authentication of the snakes on field.
Animals ; China ; DNA Primers ; genetics ; Polymerase Chain Reaction ; methods ; Reptilian Proteins ; genetics ; Snakes ; classification ; genetics

To explore the application of fetal DNA in maternal plasma for noninvasive prenatal diagnosis, the DNA template was extracted by hydroxybenzene-chloroform from 44 maternal (7-41 weeks) plasma. The Fetus-derived Y sequence DYZ-1 gene (149bp) was chosen to be amplified by PCR. The fragment was identified in all the plasma of male bearing pregnant women with the diagnostic accordance rate being 100.00%. Two of the 22 female bearing pregnant women had false positive results. Among the 44 pregnant women, the diagnostic accordance rate was 88.89% at early pregnant stage, 100.00% at medium pregnant stage, and 96.55% at late stage respectively. The final accuracy of 95.45% was obtained in all cases. It was concluded that by means of hydroxybenzene-chloroform extraction the authors of this article promoted the concentration and purity of the DNA template, and diagnosed more accurately. The results showed that free fetal DNA in the maternal plasma could be regarded as the gene resource for noninvasive prenatal diagnosis.
DNA/*blood ; DNA Primers ; Fetus ; Maternal-Fetal Exchange ; Pregnancy/*blood ; Prenatal Diagnosis/*methods ; *Sex Determination (Genetics)