Automated single nucleotide polymorphism typing using bead array in capillary tube

A low-cost and simple on-site technique for genotyping single nucleotide polymorphisms (SNPs) was developed. The technique is based on allele-specific primer PCR and the recently developed bead arrays in a single tip technique. The performance of the method was verified by genotyping four SNPs that correlate with cardiovascular diseases.     

Genotyping and phenotyping of Fusarium graminearum isolates from Germany related to their mycotoxin biosynthesis

Fusarium graminearum is the most important pathogen causing Fusarium head blight (FHB) of small cereal grains worldwide responsible for quantitative and qualitative yield losses. The presence in crops is often associated with mycotoxin contamination of foodstuff limiting its use for human and animal consumption. A collection of isolates of F. graminearum from Germany was characterized genetically and chemically for their potential to produce the B trichothecenes deoxynivalenol (DON) and nivalenol (NIV). Molecular methods with eight PCR assays were implemented based on functional Tri7 and Tri13 genes and on the tri5-tri6 intergenic region to differentiate between chemotaxonomic groups DON and NIV, resulting in a marked majority (61/63) of DON chemotypes. Mycotoxins produced on rice kernels were quantified by means of LC-MSMS including DON, NIV, 3-acetyl-DON (3-ADON), 15-acetyl-DON (15-ADON), DON-3-glucoside, fusarenon X, as well as zearalenone; all of them proving to be present in high concentration among the isolates. All DON-chemotype isolates also produced lower amounts of NIV with the amount being positively correlated (R² = 0.89) to the DON amount. 15-ADON and 3-ADON are reported to be produced simultaneously by the isolates, the former dominating over the latter in all but one isolate. Fungal biomass, was quantified via ergosterol amount on rice. It was used to calculate specific mycotoxin production per biomass of isolates, ranging from 0.104 to 1.815 mg DON mg-1 ergosterol, presenting a Gaussian distribution. Genotype and phenotype characterization revealed discrepancies with respect to mycotoxin production potential of the fungi, i.e. isolates from one chemotype were able to produce mycotoxins from other chemotypes in considerable amounts.     

Application of real-time PCR assays to genotyping of F-specific phages in river water and sediments in Japan

Genotyping of F-specific RNA phages is currently one of the most promising approaches to differentiate between human and animal fecal contamination in aquatic environments. In this study, a total of 18 river water and sediment samples were collected from the Tonegawa River basin, Japan, in order to describe the genogroup distribution of F-specific RNA and DNA phages using genogroup-specific real-time PCR assays. F-specific phages were detected in nine (100%) river water and six (67%) sediment samples. Eighty-five phage plaques were isolated from these samples and subjected to real-time PCR assays specific for the phages. F-specific RNA phages of human genogroups (II and III) were detected in 32 (38%) plaques, whereas those of animal genogroups (I and IV) were detected in 17 (20%) plaques. No correlation was observed between the genogroup distribution of F-specific RNA phages and the occurrence of human adenovirus genomes, suggesting that genotyping of the phages alone is inadequate for the evaluation of the occurrence of viruses in aquatic environments. SYBR Green-based real-time PCR assay revealed the presence of F-specific DNA phages in four (5%) plaques, which were further classified into two genogroups (fd- and f1-like phages) by sequence analysis. Thirty-two (38%) plaques were not classified as the F-specific phage genogroups, indicating the limited applicability of these real-time PCR assays to a wide range of aquatic environmental samples worldwide.     

A mixed-species microarray for identification of food spoilage bacilli

Failure of food preservation is frequently caused by thermostable spores of members of the Bacillaceae family, which show a wide spectrum of resistance to cleaning and preservation treatments. We constructed and validated a mixed-species genotyping array for 6 Bacillus species, including Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus sporothermodurans, Bacillus cereus and Bacillus coagulans, and 4 Geobacillus species, including Geobacillus stearothermophilus, Geobacillus thermocatenulatus, Geobacillus toebii and Geobacillus sp., in order to track food spoilage isolates from ingredient to product. The discriminating power of the array was evaluated with sets of 42 reference and 20 test strains. Bacterial isolates contain a within-species-conserved core genome comprising 68-88% of the entire genome and a non-conserved accessory genome comprising 7-22%. The majority of the core genome markers do not hybridise between species, thus they allow for efficient discrimination at the species level. The accessory genome array markers provide high-resolution discrimination at the level of individual isolates from a single species. In conclusion, the reported mixed-species microarray contains discriminating markers that allow rapid and cost-effective typing of Bacillus food spoilage bacteria in a wide variety of food products.     

Pulsed field gel electrophoresis typing of human and retail foodstuff Campylobacters: an Irish perspective

Campylobacter enteritis is a zoonosis, an infectious disease transmissible under normal conditions from vertebrate animals to man, presenting a major global public health burden. In this study, Pulsed Field Gel Electrophoresis (PFGE) was employed to identify common genotypes in a collection of 600 Campylobacter isolates in order to investigate if profiles obtained from retail samples of foodstuffs matched genotypes causing illness in the community in Ireland. The Campylobacters were isolated from retail foodstuffs, and cases of gastroenteritis, over the same 20-month period in three population centres in Ireland. The major observation made was of a high level of PFGE-genotype heterogeneity; 236 SmaI discrete genotypes were found in 507 strains successfully analysed. Analysis of the PFGE profiles revealed 22 common profiles amongst food isolates and those causing enteritis in humans. These cojoint PFGE genotypes indicate that 56 (38%) of the human clinical isolates are genetically related to 129 (36%) of the food isolates. The identification of these recurrent PFGE types, in the sampled Campylobacter coli and Campylobacter jejuni populations, indicates that a high proportion of Campylobacter isolates found in foods of animal origin also occur in patients with symptoms of enteritis. This data adds weight to the epidemiological hypothesis that a high proportion of human Campylobacter cases are contracted via the handling and consumption of contaminated foodstuffs, in particular poultry.     

芯片型实验室及基因组研究

芯片型实验室是９０年代后出现的新领域，它与稍早出现的测定型生物芯片相关，但其功能已超宣布是包括了分离、分析等各到基本操作。本文以在基因组研究中常用的几种技术，从ＤＮＡ测序、基因型分析和蛋白组研究三个方面，探讨了在这些领域中开始出现的芯片型推行操作元件现状和潜力。     

Genotypic characterization of Shiga toxin-producing Escherichia coli O157:H7 isolates in food products from china between 2005 and 2010

Shiga toxin-producing Escherichia coli (STEC) O157 is an important foodborne pathogen. The aims of this study were to determine genetic relatedness of STEC O157 isolated from foods in China. STEC O157 isolates from food were characterized by virulence gene typing, antibiotyping, Multi-locus sequence typing (MLST), pulsed-field gel electrophoresis analysis (PFGE), Multi-locus variable number tandem repeat analysis (MLVA), and the single nucleotide polymorphism (SNP) clade typing. Of the 30 STEC O157 isolates analyzed, all isolates harbored eae, exhA, stx1 and/or stx2 genes with stx2c subtype predominating. By MLST, they were relatively homogenous with only 4 STs. PFGE and MLVA generated 22 pulsotyples and 23 patterns, respectively, which showed considerable diversity. Only one clade 8 isolate was detected. These results indicate that STEC O157 isolates from foods in China were heterogeneous. There was no correlation between genotypic characteristics and sources of isolates. Since different subtyping methods often give different discriminatory powers, the use of more than one subtyping approach is necessary in providing a more accurate picture of the genetic diversity of STEC O157. Four isolates were from ready-to-eat meat or salads, underscores the risk of infections. There is a need for surveillance of STEC O157 in foods and clinically and implementation of prevention strategies to prevent outbreaks of STEC O157 infections in China.     

Diversity of acetic acid bacteria present in healthy grapes from the Canary Islands

The identification of acetic acid bacteria (AAB) from sound grapes from the Canary Islands is reported in the present study. No direct recovery of bacteria was possible in the most commonly used medium, so microvinifications were performed on grapes from Tenerife, La Palma and Lanzarote islands. Up to 396 AAB were isolated from those microvinifications and identified by 16S rRNA gene sequencing and phylogenetic analysis. With this method, Acetobacter pasteurianus, Acetobacter tropicalis, Gluconobacter japonicus and Gluconacetobacter saccharivorans were identified.However, no discrimination between the closely related species Acetobacter malorum and Acetobacter cerevisiae was possible. As previously described, 16S-23S rRNA gene internal transcribed spacer (ITS) region phylogenetic analysis was required to classify isolates as one of those species. These two species were the most frequently occurring, accounting for more than 60% of the isolates. For typing the AAB isolates, both the Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR and (GTG)5-PCR techniques gave similar resolution. A total of 60 profiles were identified. Thirteen of these profiles were found in more than one vineyard, and only one profile was found on two different islands (Tenerife and La Palma).     

A microfluidic platform for electrical detection of DNA hybridization

Current methods used for detection of DNA hybridization involve the use of DNA microarrays which require overnight incubation times along with bulky and expensive fluorescent scanners. Here, we demonstrate electrical detection of DNA hybridization in an oligonucleotide functionalized microfluidic channel. We use microchannels functionalized with DNA probes integrated with electrodes for measuring conductance across the channel. As beads conjugated with the target DNA passing through the channel are captured on the surface, we are able to electrically detect changes in resistance due to bead capture. Our assay can be completed in less than an hour using less than a microliter of reagent, and has the potential for extensive multiplexing. Such a device can be useful as a handheld platform in a clinical setting where one would need to rapidly genotype a small number of genes rapidly.     

Rh缺失型D--个体及其家系成员基因分型及遗传背景分析

目的分析Rh缺失型D--个体及其家系成员的基因分型及遗传背景。方法采用序列特异性引物聚合酶链反应(PCR-SSP),对Rh缺失型D--个体及其家系成员的RHD和RHCE基因的特异性序列进行扩增,并对扩增产物进行分析。结果先证者家系成员PCR结果与血清学表型基本相符,先证者RHD基因未见异常,未检出RHCE基因的特异性序列,其他家系成员均有正常表型及RHCE基因PCR产物。结论先证者RHCE基因大部分或全部缺失是造成其Rh缺失型D--的重要分子基础。先证者RHCE基因缺失,很可能其父母双方分别携带一条D--单倍型,在遗传时均将其遗传给先证者,从而形成Rh缺失型D--。