A simple method for extraction and purification of genomic DNA from dried blood spots on filter paper

We have developed an efficient and simple method for extracting and purifying genomic DNA from dried blood stored on filter paper. The quality of the genomic DNA extracted is tested by PCR amplification of a 255-bp fragment of the PAX8 gene sequence and the PCR products are determined for further genetic studies by single strand conformation polymorphism (SSCP) analysis. Larger DNA sequences of the 674-bp of the PAX8 gene and the 1,039-bp of the human beta-globin gene, a housekeeping gene, have also been amplified from the extracted DNA, thus indicating the high quality of the genomic DNA extracted by the developed method for subsequent genetic studies of any gene of interest. The method developed can also be used for the purification of genomic DNA from dried blood specimens stored under different conditions. Moreover, the genomic DNA products can be stored for long-term use due to the highly purified procedure. Therefore, the method is efficient and appropriate for the extraction and purification of genomic DNA from dried blood specimens, which has become an increasingly important tool for genetic and epidemiological studies.     

The Effect of Storage and Extraction Methods on Amplification of Plasmodium falciparum DNA from Dried Blood Spots

Extraction and amplification of DNA from dried blood spots (DBS) collected in field studies is commonly used for detection of Plasmodium falciparum. However, there have been few systematic efforts to determine the effects of storage and extraction methods on the sensitivity of DNA amplification. We investigated the effects of storage conditions, length of storage, and DNA extraction methods on amplification via three PCR-based assays using field samples and laboratory controls. Samples stored as DBS for 2 or more years at ambient temperature showed a significant loss of sensitivity that increased with time; after 10 years only 10% samples with parasite densities > 1,000 parasites/μL were detectable by nested polymerase chain reaction (PCR). Conversely, DBS and extracted DNA stored at −20°C showed no loss of sensitivity with time. Samples with low parasite densities amplified more successfully with saponin/Chelex compared with spin-column-based extraction, though the latter method performed better on samples with higher parasite densities stored for 2 years at ambient temperature. DNA extracted via both methods was stable after 20 freeze-thaw cycles. Our results suggest that DBS should be stored at −20°C or extracted immediately, especially if anticipating 2 or more years of storage.     

Allele Frequencies and Molecular Genotyping of the ABO Blood Group System in a Kuwaiti Population

The phenotypic distributions of observed numbers of ABO blood groups in a Kuwaiti sample population of 18,558 subjects are 4962 (26.7%) with A, 4,462 (24.1%) with B, 858 (4.6%) with AB, and 8,276 (44.6%) with 0. The calculated gene frequencies are 0.6678 for ABO*O, 0.1768 for ABO*A, and 0.1554 for ABO*B. Molecular genotyping of the ABO blood group system in a Kuwaiti sample population was determined using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The positions of nucleotides 258 and 700 of cDNA from A transferase were amplified by PCR. The amplified DNA was subjected to RFLP analysis to distinguish A, B, and O alleles. Blood samples of known ABO phenotype from 101 healthy unrelated Kuwaiti individuals (A, 29; B, 23; AB, 14; O,35) were used. Two DNA fragments of the ABO locus were designed to be amplified by 2 pairs of primers. To identify the 258th nucleotide, a 199- or 200-bp DNA fragment was amplified by PCR and digested with KpnI. For the 700th nucleotide, a 128-bp DNA fragment was amplified by PCR and digested with AluI. By analyzing the electrophoresis patterns,ABO genotypes were conclusively determined by examining the DNA fragments. The ABO genotypes of the known 101 samples were as follows: AA, 4.30%; AO, 24.41%; BB, 4.16%; BO, 24.2%; AB, 8.46%; and 00, 34.65%. These results were confirmed statistically using the calculated frequencies of IA, IB, and IO alleles.     

Prevalence of prothrombin gene mutation (G-A 20210 A) in general population: a pilot study.

The objective of this study was to determine the prevalence of prothrombin gene mutation in a sample population from Pakistan. Two hundred apparently healthy unrelated adults (older than 18 years) were included in the study. The sample population comprised 100 Punjabis (male 50, female 50) and 100 Pathans (male 50, female 50). Patients with a history of previous thromboembolism were excluded from the study. Five milliliters (5 mL) of whole blood was drawn in an EDTA bottle. The DNA was extracted by the standard phenol-chloroform method. The DNA was amplified between exon number 14 and the 3'-untranslated region of the prothrombin gene by a polymerase chain reaction in a thermal cycler. Amplified products were digested overnight with HindIII at 37 degrees C. The digested products were electrophoresed on 6% polyacrylamide gel. The fragments were visualized by silver nitrate staining. A heterozygous wild type and an uncut amplified product were included in the electrophoresis strip for quality control. The wild type of DNA ran as a 350-bp fragment and internal control was cut as 550- and 150-bp fragments. The abnormal prothrombin gene was cut into 350-, 322-, and 28-bp fragments. Only two cases of heterozygous prothrombin gene mutation G-A 20210A were found in the sample studied, giving an overall carrier rate of 01% (95% CI 0.4-2.4%) in the target population. Prothrombin gene mutation is present in our population but at a lower frequency than in the white population.     

Use of Blood Smears and Dried Blood Spots for Polymerase Chain Reaction–Based Detection and Quantification of Bacterial Infection and Plasmodium falciparum in Severely Ill Febrile African Children

Molecular approaches offer a means of testing archived samples stored as dried blood spots in settings where standard blood cultures are not possible. Peripheral blood films are one suggested source of material, although the sensitivity of this approach has not been well defined. Thin blood smears and dried blood spots from a severe pediatric malaria study were assessed using specific polymerase chain reaction (PCR) primers to detect non-typhoidal Salmonella (NTS; MisL gene), Streptococcus pneumoniae (lytA), and Plasmodium falciparum (18S rRNA). Of 16 cases of NTS and S. pneumoniae confirmed on blood culture, none were positive by PCR using DNA extracts from blood films or dried blood spots. In contrast, four of 36 dried blood spots and two of 178 plasma samples were PCR positive for S. pneumoniae, despite negative bacterial blood cultures, suggesting false positives. Quantitative assessment revealed that the effective concentration of P. falciparum DNA in blood films was three log orders of magnitude lower than for dried blood spots. The P. falciparum kelch13 gene could not be amplified from blood films. These findings question the value of blood PCR-based approaches for detection of NTS and S. pneumoniae, and show that stored blood films are an inefficient method of studying P. falciparum.     

聚合酶链反应用于鉴别恶性疟原虫不同分离株的研究

用恶性疟原虫主要裂殖子表面抗原基因序列（ＭＳＡ－１）为引物的聚合酶链反应（ＰＣＲ）技术检测恶性疟原虫感染。用此方法扩增实验室体外培养的ＦＣＣ１／ＨＮ株恶性疟原虫，显示１条３００ｂｐ的ＤＮＡ片断，而对实验室培养的巴布亚新几内亚ＦＣＱ－２７株则显示１条４４０ｂｐＤＮＡ条带。用此方法检测１５份采自云南中缅边界的恶性疟血样均能扩增出ＤＮＡ条带，但不同血样的ＤＮＡ条带的分子量不同，部分血样还存在１条以上的ＤＮＡ条带。在同时扩增的１０份正常人血样和１０份采自江苏间日疟流行区的现症间日疟血样中均没有发现ＤＮＡ条带。表明此方法具有很高的种和株的特异性。     

A newly discovered Anaplasma phagocytophilum variant in rodents from southeastern China

Anaplasma phagocytophilum was detected by polymerase chain reaction in 13 (14.1%) of 92 rodents captured from a mountainous area of Zhejiang Province in southeastern China. The nucleotide sequences of 1442-bp, nearly entire 16S rRNA gene amplified from these rodents, had 100% identity, but varied from all known corresponding sequences of A. phagocytophilum deposited in GenBank. To further identify and classify the variant, fragments of 357-bp partial citrate synthase gene (gltA), 849-bp major surface protein 4 gene (msp4), and 443-bp groESL heat-shock operon gene, were amplified and analyzed. The nucleotide sequences of the partial gltA gene amplified from the rodents were identical to each other, but distinct from previously reported A. phagocytophilum sequences,as were msp4 and groESL. These findings indicate that the newly discovered agent represents a novel A. phagocytophilum variant.     

Application of multiplex pcr for species discrimination using individual metacercariae of Paragonimus occurring in Thailand

A total of 6 lung fluke species have been documented in Thailand, of which P. heterotremus is the most important, since it affects humans. Although P. westermani is found as metacercariae in the same crab species as P. heterotremus in Thailand, human infections with P. westermani have not been confirmed. To accurately discriminate between the individual metacercariae of these two species, we established a multiplex PCR method. Using this method, two products each were amplified from the metacercarial DNA samples of P. heterotremus (ca. 310 and 520 bp) and P. westermani (ca. 140 and 520 bp). In contrast, 520-bp products alone were found to be generated from the DNA samples of P. siamensis, P. bangkokensis and P. harinasutai, 3 other species of lung flukes known to occur in Thailand. Digestion of these 520-bp products with the restriction enzyme ScrFI could unequivocally discriminate species by the number and size of the produced band(s): 3 bands (ca. 60, 210 and 250 bp) for P. harinasutai, 2 bands (ca. 250 and 270 bp) for P. bangkokensis, and an uncut band (520 bp) for P. siamensis. The established multiplex PCR used in combination with restriction enzyme digestion (PCR-RFLP with ScrFI) is effective for discriminating the 5 different species of lung flukes occurring in Thailand, even at the metacercarial stage.     

应用FTA/PCR检测粪便中隐孢子虫的实验研究

目的 建立用FTA/PCR检测粪便中隐孢子虫的技术,并与常用的商业化的粪便DNA抽提试剂盒进行比较.方法 选择经病原学检测已经确诊的隐孢子虫阳性和阴性粪便,分别采用FTA卡和商业化DNA抽提试剂盒抽提粪便样本中DNA,进行巢式PCR扩增,对PCR阳性产物进行测序并利用BLAST在NCBI上与GenBank数据库进行比对,做同源性分析,确定虫种.结果 应用商业化DNA抽提试剂盒抽提DNA,无论是否反复冻融破壁,2个阳性对照样本扩增出目的 片段,另3个阳性样本未扩增出特异性条带.样本纯化后应用FTA卡抽提DNA进行PCR检测,所有阳性粪样均扩增出830 bp左右的目的 片段,通过测序和比对,其中2个为贝氏隐孢子虫,1个为火鸡隐孢子虫.结论 应用FTA进行粪便样本中隐孢子虫DNA的抽提方法具有简单有效、快速灵敏、准确可靠等特点,可以应用于粪便中隐孢子虫的检测.     

Isolation of fetal DNA from nucleated erythrocytes in maternal blood.

Fetal nucleated cells within maternal blood represent a potential source of fetal genes obtainable by venipuncture. We used monoclonal antibody against the transferrin receptor (TfR) to identify nucleated erythrocytes in the peripheral blood of pregnant women. Candidate fetal cells from 19 pregnancies were isolated by flow sorting at 12 1/2-17 weeks gestation. The DNA in these cells was amplified for a 222-base-pair (bp) sequence present on the short arm of the Y chromosome as proof that the cells were derived from the fetus. The amplified DNA was compared with standardized DNA concentrations; 0.1-1 ng of fetal DNA was obtained in the 20-ml maternal samples. In 7/19 cases, a 222-bp band of amplified DNA was detected, consistent with the presence of male DNA in the isolated cells; 6/7 of these were confirmed as male pregnancies by karyotyping amniocytes. In the case of the female fetus, DNA prepared from samples at 32 weeks of gestation and cord blood at delivery also showed the presence of the Y chromosomal sequence, suggesting Y sequence mosaicism or translocation. In 10/12 cases where the 222-bp band was absent, the fetuses were female. Thus, we were successful in detecting the Y chromosomal sequence in 75% of the male-bearing pregnancies, demonstrating that it is possible to isolate fetal gene sequences from cells in maternal blood. Further refinement in methodology should increase sensitivity and facilitate noninvasive screening for fetal gene mutations.     

Are human herpes viruses or measles virus associated with esophageal achalasia?

In order to test the hypothesis that esophageal achalasia may be due to neurotropic viral damage to the esophageal myenteric plexus, esophageal tissue with or without achalasia was analyzed by polymerase chain reaction for the presence of human herpes virus DNA or measles virus RNA. The DNA and RNA were extracted from the esophageal muscle of 12 patients with achalasia and six patients with upper esophageal carcinoma. Peripheral blood mononuclear cells from eight adult volunteers and two samples of umbilical blood mononuclear cells were also used as controls. PCR amplification with a pair of primers specific for herpes simplex type 1 and 2 viruses identified 92-bp fragments in nearly all specimens, including those without achalasia. Each 92-bp fragment was confirmed to be identical to a single herpes simplex virus sequence by automated DNA sequence analysis. No amplification for five other herpes viruses or measles virus was detected. Therefore, a specific viral etiology for achalasia was not identified in this study.     

武汉市HIV-1相关基因序列分析及亚型分布

目的研究武汉市HIV感染人群中的HIV毒株的亚型分布特点和流行规律。方法采集武汉市60名已被确认为HIV-1感染者的抗凝全血样品,提取前病毒DNA,用巢式聚合酶链反应方法（nested-PCR）扩增病毒膜蛋白env基因的C2-V5区及gag基因的部分区段,对PCR纯化产物直接测序,并应用GCG软件对序列进行分析。结果通过PCR扩增得到60份样品的结果,其中env基因序列45份、gag基因序列52份。依据env和gag区基因序列,与HIV-1各个亚型国际参考株比较,通过系统进化分析,最后确定武汉市样品分属5个亚型,分别为HIV-1B亚型中的泰国B（B’）亚型32份,流行重组型CRF07-BC12份,流行重组型CRF01-AE9份,A亚型1份和C亚型6份。结论武汉市存在多种HIV-1亚型,应加强对HIV-1毒株亚型变异的监测,及时调整防治策略。     

黑龙江全沟硬蜱中检测出类似人粒细胞埃利希体的病原体DNA

目的：寻找我国蜱中人粒细胞埃利希体感染存在的病原学证据。方法：应用从人粒细胞埃列希体16 rRNA基因构建的特异引物进行半套式PCR,检测蜱标本中埃利希体DNA。然后对PCR扩增产物进行克隆和序列测定,与已知序列进行同源性比较。结果：从黑龙江采集的全沟硬蜱（Ixodes persulcatus）中扩增出特异DNA片段,计算最小阳性率为0.8％。对919bp的扩增产物进行序列分析,证实为埃利希体DNA,与美国人粒细胞埃利希体分离株对应序列比较,相差4个核苷酸。结论：这是首次证明我国有类似人粒细胞埃利希体的病原体存在。表明我国北方林区可能存在人粒细胞埃利希体感染垢自然疫源地。     

陕西省HIV-1流行株膜蛋白基因 C2-V3区序列特征和亚型分析

目的了解陕西省HIV-1毒株的流行情况和亚型特征.方法用套式聚合酶链式反应(Nested-PCR)对6份采集于陕西省经确认为HIV-1感染者或艾滋病病人外周血淋巴细胞(PBMC)提取核酸,从6份样品中获得了HIV-1膜蛋白(ENV)基因的核酸片段进行扩增,并测定和分析了C2-V3及其邻区共312个核苷酸序列.结果 6份血样中,2份为HIV-1A亚型毒株感染(SHX7、SHX8);4份为HIV-1B'亚型(泰国B'亚型)毒株感染(SHX1、SHX5、SHX6、SHX9).SHX1、SHX5、SHX6、SHX9彼此间基因离散率为5.62%,SHX7与来自卢旺达的U08794之间的基因离散率仅为2.41%.结论陕西省目前存在HIV-1 A、B'两种亚型的毒株,HIV-1 B'亚型由邻近地区传入,HIV-1 A亚型为与非洲人接触传入.     

Development of a duplex-polymerase chain reaction for rapid detection of pathogenic Leptospira

A duplex-polymerase chain reaction (PCR) for the rapid detection of pathogenic leptospires was developed by using two sets of newly designed primers which amplified in the same reaction two different DNA fragments simultaneously: 279-bp of LipL32 and 430-bp of 16S rRNA. For DNA extraction from bacterial cultures, the silica-based spin column method was found to be more suitable and was selected for the extraction of DNAs from all 92 bacterial strains including 56 strains of pathogenic Leptospira, 15 strains of non-pathogenic Leptospira and 21 other strains of bacteria. The PCR products were analyzed by agarose gel-electrophoresis with confirmation by Southern and dot hybridization using synthetic DNA probe prepared from LipL32 gene of a pathogenic reference strain, L. interrogans serovar pyrogenes. The duplex-PCR allowed detection of two products of 279 bp and 430 bp in all pathogenic Leptospira. Non-pathogenic Leptospira generated a single product of 430 bp. Other bacterial strains failed to reveal any amplification products. As little as 1 pg of pure DNA corresponding to 100 cells could be detected by agarose gel-electrophoresis, and 1-10 fg of pure DNA by hybridization.     

Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments. METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD) with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated, purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data. RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene. CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcin-ogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis.     

间日疟原虫云南分离株传播阻断疫苗候选抗原Pvs 28基因多态性分析

目的分析我国疟疾混合流行区云南分离株间日疟原虫（P．v）传播阻断疫苗候选抗原Pvs28基因特点。方法收集云南省血样17份；提取疟原虫基因组DNA；PCR扩增Pvs28基因；基因测序；DnaSP version4．0软件进行基因多态性分析。结果成功扩增Pvs28全长基因17个序列。与标准株Sal—I比较，检测出7个错义突变，7个基因型和7种氨基酸型。云南P.v分离株核苷酸多态性n值为0．0044。若不考虑重复片段拷贝数的差异，云南P．v分离株和湖北P．v分离株Pvs 28蛋白主导氨基酸型完全一致，即V^14-L^52-L^98-E^105-L^115-S^14-I^122。与泰国P．v分离株比较。我国主导基因型突变位点完全包含在泰国P．v分离株突变位点中。结论以Sal—I Pvs28为基础建立的传播阻断疫苗能够克服云南P．v分离株Pvs28抗原多样性而发挥传播阻断作用，提示间日疟原虫传播阻断疫苗在我国具有良好的应用前景。     

Simple method for long-term copro-preservation of Cryptosporidium oocysts for morphometric and molecular analysis

Preservation of Cryptosporidium oocysts in faecal specimens containing 75% ethanol is suitable for subsequent morphometric and molecular analysis. No significant morphologic alteration occurred after storage at ambient temperatures, ranging from 22 to 38 degrees C, for more than 2 years. After washing, sugar floatation and DNA extraction, a nested polymerase chain reaction targeting the small subunit ribosomal RNA gene successfully amplified Cryptosporidium DNA in all 15 isolates examined. The sensitivity of detection by polymerase chain reaction (PCR) was found to be as high as 1.25 oocysts per reaction (mean=3.01, SD=1.14). Importantly, a 2.2-kb of the complete DNA sequence of a gene encoding Cryptosporidium thrombospondin-related adhesive protein (TRAP-C1) was also consistently amplified by PCR in all isolates. The PCR-amplified product can be used as a good template for sequencing. Therefore, this simple procedure should be useful for epidemiological analysis of clinical samples from outbreaks, endemic or sporadic cases of cryptosporidiosis when long-term storage of oocysts is required.     

Molecular epidemiology of Theileria parva in the field

Molecular tools based on seminested RFLP-PCR techniques to characterize field parasites in bloodspots dried on filter paper permitted investigation of the extent and the dynamics of diversity of Theileria parva populations in the field. Parallel molecular studies explored the long-term genome stability of various isolates by probing Southern blots of EcoRI digested total genomic DNA with four different reference nucleic acid probes. Three polymorphic single copy loci encoding for antigen genes were developed for seminested PCR detection in order to apply them for a multilocus approach in population genetic studies. Seven alleles were identified for the polymorphic immunodominant molecule (PIM) locus by using restriction enzymes, and 4 alleles each for the p150 and p104 loci. A simple DNA extraction method gave good results in amplifying these loci from carrier animals using samples of blood dried on filter papers. Results from probing Southern blots of cultures taken at sequential timepoints indicate relative genome stability in T. parva in comparison to other parasitic protozoa such as Plasmodium. Comparatively homogeneous profiles in sympatric isolates from Zambia were identified using all four probes and PCR amplified products which contrasted with the variety found amongst Kenyan stocks. Preliminary characterization of T. parva field samples from the Southern Province of Zambia strongly suggest clonal expansion of one of the components of a non-Zambian trivalent vaccine used on a limited scale in the Province from 1985 until 1992.