PURPOSE: Although the polymorphisms of erythrocyte complement receptor type 1 (CR1) in patients with malaria have been extensively studied, a question of whether the polymorphisms of CR1 are associated with severe malaria remains controversial. Furthermore, no study has examined the association of CR1 polymorphisms with malaria in Chinese population. Therefore, we investigated the relationship of CR1 gene polymorphism and malaria in Chinese population. MATERIALS AND METHODS: We analyzed polymorphisms of CR1 gene rs2274567 G/A, rs4844600 G/A, and rs2296160 C/T in 509 patients with malaria and 503 controls, using the Taqman genotyping assay and PCR-direct sequencing. RESULTS: There were no significant differences in the genotype, allele and haplotype frequencies of CR1 gene rs2274567 G/A, rs4844600 G/A, and rs2296160 C/T polymorphisms between patients with malaria and controls. Furthermore, there was no association of polymorphisms in the CR1 gene with the severity of malaria in Chinese population. CONCLUSION: These findings suggest that CR1 gene rs2274567 G/A, rs4844600 G/A, and rs2296160 C/T polymorphisms may not be involved in susceptibility to malaria in Chinese population.
Adult ; Alleles ; Asian Continental Ancestry Group ; Case-Control Studies ; China ; Erythrocytes/parasitology ; Female ; Genetic Predisposition to Disease ; Genotype ; *Haplotypes ; Humans ; Malaria/ethnology/*genetics ; Male ; Middle Aged ; Polymorphism, Single Nucleotide/*genetics ; Promoter Regions, Genetic/*genetics ; Receptors, Complement/blood/*genetics ; Taq Polymerase

In order to develop a rapid detection kit for novel avian influenza virus (AIV) subtype H7N9, two sets of specific primers and probes were designed based on the nucleotide sequences of hemagglutinin antigen (HA) and neuraminidase antigen (NA) of novel H7N9 virus (2013) available in GenBank to establish the method of TaqMan probe-based multiplex real-time RT-PCR for rapid detection of AIV subtype H7N9. The primer and probe of HA were for all H7 subtype AIVs, while the primer and probe of NA were only for novel N9 subtype AIVs. The results showed that this method had high sensitivity and specificity. This method was applicable to the testing of positive standard sample with a minimum concentration of 10 copies/microL; it not only distinguished H7 subtype from H1, H3, H5, H6, and H9 subtypes, but also distinguished novel N9 subtype from traditional N9 subtype. A total of 2700 samples from Zhuhai, China were tested by this method, and the results were as expected. For the advantages of sensitivity and specificity, the method holds promise for wide application.
Animals ; Birds ; virology ; Influenza A Virus, H7N9 Subtype ; genetics ; isolation & purification ; physiology ; Influenza in Birds ; prevention & control ; virology ; Real-Time Polymerase Chain Reaction ; methods ; Species Specificity ; Taq Polymerase ; metabolism ; Time Factors

BACKGROUND: Accurate typing of Duffy blood group is important because anti-Duffy antibodies cause hemolytic transfusion reaction and hemolytic disease of the newborn. The aim of this study was to evaluate a new genotyping method using high resolution melting (HRM) analysis, a rapid and inexpensive approach for high-throughput Duffy genotyping. METHODS: A total of 20 unrelated Korean blood samples were obtained and an African-black sample was used for GATA control. Phenotyping was performed by hemagglutination (DiaMed AG, Switzerland). GATA and FYA/B PCR products were obtained by PCR-restriction fragment length polymorphism (RFLP) using Taq DNA polymerase (Promega, WI) and enzymes BanI and StyI (New England Biolab, UK). For HRM, PCR amplification was performed using LightCycler 480 ResoLight Dye (Roche, USA) and Lightcycer 480 (Roche, USA). RESULTS: Phenotyping and genotyping data using PCR-RFLP and HRM analysis were compared. Different types of HRM curves were obtained according to genotypes, FYA/FYA, FYB/FYB, and FYA/FYB, and to GATA mutations, homozygote FYB-33T (T/T), heterozygote FYB-33T/33C (T/C), and homozygote FYB-33C (C/C). Phenotypes 18 Fy(a+b-), 1 Fy(a+b+), 1 Fy(a-b+), and 1 Fy(a-b-) showed complete concordance with genotyping methods. Fy(a-b-) sample was found to be a FYB-33C homozygote by both genotyping methods. CONCLUSION: Phenotyping and genotyping showed concordant results and both genotyping methods using PCR-RFLP and HRM analysis showed good agreement in finding mutation in GATA and FY gene coding regions. HRM analysis is suitable and reliable for high-throughput screening for Duffy genotyping.
Antibodies ; Blood Group Antigens ; Blood Group Incompatibility ; Clinical Coding ; England ; Freezing ; Genotype ; Hemagglutination ; Heterozygote ; Homozygote ; Humans ; Infant, Newborn ; Mass Screening ; Phenotype ; Polymerase Chain Reaction ; Taq Polymerase

OBJECTIVETo investigate the optimization system of SRAP-PCR molecular marker technology in the analysis on Pinellia ternata.

METHODSRAP-PCR reaction system for P. ternata was optimized by L16 (5(4)) orthogonal design with five elements (dNTPs, Mg2+, the template DNA, primers, Taq enzyme) and four standards.

RESULTThe most suitable forward primer for SRAP for Pinellia ternata was 5'-TGAGTCCAAACCGGAAG-3', while the reverse primer was 5'-GACTGCGTACGAATTACG-3'. The optimized reaction system contained 70 ng DNA template, 0.9 micromol x L(-1) primer, 0.20 mmol x L(-1) dNTP s, 1.5 - 2.0 mmol x L(-1) Mg2+, and 2 U Taq enzyme.

CONCLUSIONSRAP-PCR system for P. ternata is established to lay a foundation for future construction of SRAP genetic map of P. ternata.

China ; DNA Primers ; genetics ; DNA, Plant ; genetics ; Electrophoresis ; Magnesium ; metabolism ; Nucleic Acid Amplification Techniques ; methods ; Nucleotides ; genetics ; Pinellia ; genetics ; Polymerase Chain Reaction ; methods ; Reproducibility of Results ; Taq Polymerase ; metabolism ; Templates, Genetic

OBJECTIVE: To develop a rapid, accurate and economical real time fluorescence PCR method with TaqMan probe technology to detect the X chromosome single nucleotide polymorphism (X-SNP). METHODS: TaqMan probes and polymerase chain reaction primers were respectively designed according to the 13 X-SNP. Then, the X-SNP were genotyped after the amplification by real time fluorescence PCR. RESULTS: All the loci follow the Hardy-Weinberg equilibrium. The polymorphic information content for 13 distinct loci varied between 0.3497 and 0.3750 while the heterozygosity ranged from 0.4537 to 0.5021. A real time fluorescent PCR method based on TaqMan probe was successfully developed and the results were accordant with those analyzed by DNA sequencing of the 13 X-SNP. CONCLUSION The allele specific real time fluorescence PCR based on TaqMan probe is a sensitive, simple technology and suitable for rapid analysis of XSNP. All the loci show highly polymorphic and may be potential in forensic genetics.
Alleles ; Asian People/genetics* ; China/ethnology* ; Chromosomes, Human, X/genetics* ; DNA/genetics* ; DNA Probes ; Female ; Fluorescent Dyes ; Forensic Genetics ; Gene Frequency ; Genotype ; Humans ; Male ; Polymerase Chain Reaction/methods* ; Polymorphism, Single Nucleotide/genetics* ; Sensitivity and Specificity ; Taq Polymerase

OBJECTIVEIn this study, orthogonal design was used to optinize DDRT-PCR amplification system on Pinellia ternata microtubers in vitro in five factors four levels respectively.

METHODP. ternata stems and microtubers in vitro were selected as explants. The effects of five kinds of factors were studied by orthogonal design method including emplate cDNA, Mg2+, dNTPs, primers and Taq DNA polymerase, and in order to establish the optimum DDRT-PCR system of P. ternata microtubers in vitro.

RESULT AND CONCLUSIONA satisfactory DDRT-PCR technique system for P. ternata microtubers in vitro with desirable repeatability and polymorphic bands was established. In a total volume of 20 microL DDRT-PCR system, it contained 10 x buffer, 150 micromol L(-1) dNTPs, 2 micromol L(-1) anchor primer, 1 micromol L(-1) arbitrary primer, 2.5 mmol L(-1) Mg2+, 0.6 U Taq DNA polymerase and 2.5 microg template cDNA. The effect of the five factors was in sequence of Taq DNA polymerase > template cDNA > dNTPs > Mg2+ > Primers. The optimum DDRT-PCR system will provide scientific reference basis for studying effecting character of P. ternata microtubers associated with genes expression.

DNA, Complementary ; genetics ; DNA, Plant ; genetics ; Electrophoresis, Polyacrylamide Gel ; Pinellia ; genetics ; Plant Tubers ; genetics ; Polymerase Chain Reaction ; methods ; Silver Staining ; Taq Polymerase ; genetics

OBJECTIVETo develop a real-time polymerase chain reaction(PCR) based on TaqMan technology by using a new MGB probe for detecting enterotoxigenic Escherichia coli (ETEC) in paper.

METHODSPrimers and MGB probe were designed in the ecoding region of heat-stable toxin of ETEC. Real-time PCR detected ETEC by using the exterior standard method with protracting standard curves. The specificity, sensitivity, accuracy, stability of real-time PCR system was evaluated. An internal negative antithesis was added to the real-time PCR system in order to get rid of the false positive of system. Using UNG enzyme expelled the contamination of PCR reaction.

RESULTSPrimers and MGB probe were suited to the Real-time PCR. The assay showed that the method was quick, special, sensitive and stable. The real-time PCR system could detect ETEC in a large scale. The assay might be finished in two hour.

CONCLUSIONThese observations suggested that real-time PCR based on MGB probe should be an excellent candidate for a standard ETEC detection method.

Bacterial Toxins ; isolation & purification ; DNA Primers ; DNA Probes ; DNA, Bacterial ; Enterotoxigenic Escherichia coli ; isolation & purification ; Molecular Probe Techniques ; Polymerase Chain Reaction ; methods ; Taq Polymerase

UNLABELLEDWe designed a pair of specific primers and a TaqMan fluorescent probe targeting the toxR gene of Vibrio parahaemolyticus (VP). After optimizing the conditions, the specialty, sensitivity and reproducibility of the detection method were evaluated.

RESULTS(1) the developed real-time PCR assay protocol detected only VP and was not affected by other normal food pathogens such as Staphylococcus aureus, Salmonela, Listeria monocytogenes. (2) the limit of detection was 25 copies of toxR gene in the detected samples, and the sensitivity of pure cultures and simulated food samples was 21 cfu/mL and 210 cfu/g. (3) the developed protocol of real-time PCR assay had a high reproducibility, and the sample's variation was 0.9% and 1.3% within the same sample and between tests. (4) the standard curve had a good linearity when the gene quantity was between 2.5x10(1) and 2.5x10(6) copies. The developed detection assay targeting the toxR gene can quantitatively detect VP in only 3 hours, and thus is an efficacious method for the detection of Vibrio parahaemolyticus.

Bacterial Proteins ; genetics ; DNA-Binding Proteins ; genetics ; Fluorescent Dyes ; metabolism ; Gene Targeting ; Polymerase Chain Reaction ; methods ; Sensitivity and Specificity ; Taq Polymerase ; metabolism ; Transcription Factors ; genetics ; Vibrio parahaemolyticus ; genetics ; isolation & purification

Pseudomonas aernginosa (PA) is one of the most universal pathogens in clinical diagnosis, and conventional detection assay has many disadvantages. In this research, a pair of specific primers and a TaqMan fluorescent probe were designed in the conservative region of ETA gene by the method of bioinformatics analysis, the detection method for PA was successfully developed. Different gradient concentrations of PA DNA and various pathogen DNA were amplified by fluorescence quantitative PCR (FQ-PCR) to confirm the specificity and sensitivity of the developed method. Results showed that the developed detection assay is more sensible and specific by comparison to the conventional FQ-PCR method, and it is valuable for research and application prospects.
ADP Ribose Transferases ; genetics ; Bacterial Toxins ; genetics ; DNA, Bacterial ; analysis ; Exotoxins ; genetics ; Fluorescent Dyes ; Fluorometry ; methods ; Polymerase Chain Reaction ; methods ; Pseudomonas aeruginosa ; genetics ; isolation & purification ; Sensitivity and Specificity ; Taq Polymerase ; Virulence Factors ; genetics

BACKGROUNDTo develop a rapid and more sensitive TaqMan RT-PCR assay specific for Banna virus.

METHODSTotal RNA of strains of Banna virus and other arboviruses were extracted and reverse transcribed to cDNAs. With the cDNAs as templates, the TaqMan RT-PCR assay was developed and optimized on ABI 7300 apparatus for specific-detection of Banna virus. The sensitivity, specificity and the possibility of this assay to detect Banna virus in pools of mosquitoes. Meanwhile, human sera samples added with different dilutions of Banna virus culture medium supernatant were evaluated.

RESULTSAll the collected 12 Banna virus strains in our country were detected as positive, while the results of other arboviruses such as Japanese encephalitis virus (JEV), Batai virus, Sindbis virus and Orbiviruses were negative. This assay was more than 100 times sensitive than that of traditional PCR. About 0.5 CCID-50 of Banna virus in 50 microl samples could be detected with this assay. The sensitivity decreased by about 10 times when the dsRNA was denatured in 65 degrees C instead of 99 degrees C, and also when the virus seeds were kept at room temperature for 1 day or 1 week at 4 degrees C. There was no significant difference in the results of Banna virus detection between artificial human serum samples and positive control virus. Six were detected as positive for Banna virus-specific nucleic acids in 112 pools of mosquitoes, while 3 was positive with virus isolation.

CONCLUSIONThe Banna virus-specific TaqMan RT-PCR assay was proved to be highly sensitive, specific and showed a good reproducibility; the assay may be applied for surveillance of this virus in clinical samples and pools of mosquitoes screening.

Animals ; Coltivirus ; genetics ; isolation & purification ; Culicidae ; virology ; Humans ; RNA, Viral ; genetics ; isolation & purification ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; methods ; Taq Polymerase ; metabolism