Rapid identification of medicinal herbs through plant Direct-PCR / 药学学报

Direct-PCR technology was using a 15 minutes heat-lysis step instead of DNA extraction to get DNA templates with small amount of plant materials followed by sensitive PCR process to amplify target genes. In order to facilitate DNA barcoding in medicinal herb identification with Direct-PCR, we collected different tissues from 80 medicinal plants as material to amplify the ITS fragments. Through optimizing the PCR reaction, ITS of 80 plant samples was all successfully amplified. PCR products were sequenced and to do Blast analysis. These results suggest that Direct-PCR would improve the efficiency of DNA barcoding in the application of medicinal herb molecular authentication.

Establishment and application of multiplex direct PCR for rapid detection of common food borne pathogens in swine products / 中国人兽共患病学报

We established a multiplex direct PCR for rapid detection of E.coli,Salmonella,Staphylococcus aureus,Listeria and Yersinia enterocolitica bacteria.Multiplex direct PCR primers were designed according to gene sequences of phoA (E.coli),inv A (Salmonella),nuc (S.aureus),hl y (Listeria),and ail (Y.enterocolitica).After the multiplex direct PCR were established,the specificity and sensitivity of primers were detected.Then,multiplex direct PCR was applied to examine 60 swine product samples,the detection specificity,accuracy and positive predictive value were calculated compared with the gold standard culture method.Results showed that multiplex direct PCR primers could be used for specific detection of E.coli,Salmonella,S.aureus,Listeria and Y.enterocolitica,with the minimal detectable limit of 10,1,100,1 and 1 CFU,respectively.For the examination of 60 swine product samples using multiplex direct PCR,15 were positive for E.coli,6 positive for Salmonella,21 positive for S.aureus,20 positive for Listeria,and 35 positive for Y.enterocolitica,with all positive detection rates higher than that of culture.The total detection sensitivity was 100％,accuracy was 94％,and positive predictive value was 81.44％.Multiplex direct PCR could be used for specific and sensitive detection of common food-borne pathogens,and the testing time was shorten to be 3 hours because of saving time for template extraction.Multiplex direct PCR might serve the detection of food-borne pathogens in food safety risk monitoring much better.

A new methodology of DNA polymorphism detection from standard long gun / 中国法医学杂志

Objective A new methodology was established to efficiently obtain the genotype of DNA remained on standard long gun. Methods Direct PCR and silicon membrane method were combined to detect DNA polymorphism of a total of 240 samples at 5 different positions from 48 standard long guns. Results Combining direct PCR and silicon membrane method, we obtained full DNA profiles in 42 out of 48 standard long guns, with a detection rate up to 87.50%. Conclusion The results demonstrate that the combination of direct PCR and silicon membrane method provide a quick and accurate way to detect DNA polymorphism on the standard long gun.

Identifying 1 strain of conditional pathogenic Ochrobactrum by 16S rRNA gene sequencing / 国际检验医学杂志

Objective To explore a rapid bacterial identifying method based on the 16S rRNA gene sequence analysis technology to provide the scientific basis for the diagnosis and treatment of unknown pathogenic bacteria.Methods The pure colonies were iso-lated and cultured directly from a clinical patient′s sputum sample.The colony as a template for PCR amplification with universal primers to amplify 16S rRNA gene fragments of unknown bacteria.The product of PCR was sequenced directly,then the sequence result was compared by using the BLAST of NCBI and the pathogen was identified based on the sequence homology.Results 1 strain of unknown pathogen was identified as ochrobactrum by this test and confirmed by ABI bacterial rapid identification sys-tem.Conclusion This study simplifies the isolation and identification procedures of unknown pathogen from the clinical samples and establishes a simple method for the rapid identification of pathogens by using 16S rRNA gene amplification.

Comparison of sxx commercially-available dna polymerases for direct ccr / Comparacao de seis polimerases de DNA disponiveis comercialmente para o PCR direto

SUMMARY The use of a “direct PCR” DNA polymerase enables PCR amplification without any prior DNA purification from blood samples due to the enzyme's resistance to inhibitors present in blood components. Such DNA polymerases are now commercially available. We compared the PCR performance of six direct PCR-type DNA polymerases (KOD FX, Mighty Amp, Hemo KlenTaq, Phusion Blood II, KAPA Blood, and BIOTAQ) in dried blood eluted from a filter paper with TE buffer. GoTaq Flexi was used as a standard DNA polymerase. PCR performance was evaluated by a nested PCR technique for detecting Plasmodium falciparum genomic DNA in the presence of the blood components. Although all six DNA polymerases showed resistance to blood components compared to the standard Taq polymerase, the KOD FX and BIOTAQ DNA polymerases were resistant to inhibitory blood components at concentrations of 40%, and their PCR performance was superior to that of other DNA polymerases. When the reaction mixture contained a mild detergent, only KOD FX DNA polymerase retained the original amount of amplified product. These results indicate that KOD FX DNA polymerase is the most resistant to inhibitory blood components and/or detergents. Thus, KOD FX DNA polymerase could be useful in serological studies to simultaneously detect antibodies and DNA in eluents for antibodies. KOD FX DNA polymerase is thus not limited to use in detecting malaria parasites, but could also be employed to detect other blood-borne pathogens. .

RESUMO O propósito deste estudo foi avaliar 6 polimerases de DNA disponíveis comercialmente que são resistentes aos inibidores do PCR para uma amplificação potencial de DNA de amostras de sangue total. O DNA genômico do parasita humano da malária, Plasmodium falciparum, foi analisado sob condições que incluíram os componentes inibidores do sangue extraído de sangue ressacado em papel de filtro. Nossos resultados sugerem que a polimerase KOD FX DNA é superior a outras polimerases. .

Diagnosis value of direct PCR to acanthamoeba keratitis / 中华实验眼科杂志

Background Acanthamoeba keratitis is a sort of serious infectious eye disease with high causing-blindness rate.Acanthamoeba keratitis often is misdiagnosed as fungal keratitis or viral keratitis in the early stage.Because conventional clinical diagnosis methods show a low specificity and take a long time,timely treatment often is delayed.Conventional PCR does not apply well because the lesion sample is not enough to extract DNA.However,direct PCR can amplify 18S rRNA conserved sequence of acanthamoeba keratitis without the extraction of DNA.Objective This study was to discuss the feasibility for rapid diagnosis of acanthamoeba keratitis using direct PCR to amplify the gene 18S rRNA fragment.Methods Ten acanthamoeba strains were isolated from 10 eyes with acanthamoeba keratitis in Qingdao Eye Hospital.The sensitivity of the direct PCR assay was tested using different numbers of amoebas.The specificity of the assay was tested using DNA extracted from acanthamoeba,candida albicans,pseudomonas aeruginosa,herpes simplex virus-1 (HSV-1) and normal human corneal epithelial cell.Acanthamoeba keratitis models were established using infected method in clean 6-week-old female BALB/c mice.Corneal lesion samples were obtained 1 day,3,5,7,10,15 days after modeled.The effectivity and feasibility of the direct PCR assay for rapid diagnosis of acanthamoeba keratitis were evaluated and compared with culture method,corneal smear examination and real-time PCR.Results Direct PCR primers could only amplify DNA of acanthamoeba rather than other pathogens,and 10 stains of acanthamoeba were detected at least in each sample.During the development of acanthamoeba keratitis in the mice,the diagnosis positive rate of direct PCR was 80.0％,90.0％,80.0％,70.0％,70.0％ and 50.0％ in 1 day,3,5,7,10,15 days after modeled with the total positive rate 73.3％,which was higher than 31.7％ of culture method,56.7％ of corneal smear examination and 61.7％ of realtime PCR,with a significant difference between the direct PCR and culture method (P =0.005),but no significant difference was seen in the total positive rate between the direct PCR and real-time PC R (P =0.172) or corneal smear examination (P =0.056).Conclusions The direct PCR assay is a simple,rapid,highly specific and sensitive method for the rapid diagnosis of acanthamoeba keratitis,especially for the limited lesion sample.

Multiplex PCR assay for direct detection of diarrheagenic escherichia coli from clinical stool specimens

Background: To distinguish the different types of pathogenic E. coli with other non-pathogenic E.coli in the intestine is extremely important in diagnosis. Up to date there are at least six types of E. coli that causes diarrhea. Objectives: We have designed a multiplex PCR assay for the direct detection of 6 categories of diarrheagenic Escherichia coli. Subjects and method: This techniques proved to be specific and rapid for detecting virulence genes from Shiga toxin-producing (stx and eae), enteropathoogenic (eae), enterotoxigenic (elt, est), ennteroinvasive (ipaH), enteroaggregative (aggR), and diffuse adherent (daaE) Esscherichia coli. The technique was applied to 295 clinical stool specimens. Results: The highest prevalence is EAggEC with 51 positive samples.(17.29%), 48 EIEC (16.27%), 17 EPEC (5.76%), 8 ETEC (LT) (2.71%), 5 ETEC (ST) (1.69%), 1 DAEC (0.34%), no STEC positive and 19 mix infections (6.44%). Conclusion: Multiplex PCR assay is a quick and highly accuurate technique. It is not only specific but can also amplify 7 virulence genes of diarrrheagenic E.coli at the same time. This method would offer an effective alternative to traditional culture methods for the identification and differentiation of human diarrhaegenic Escherichia coli.