Showing papers in "Molecular and Cellular Probes in 2006"

TL;DR: Examination of dilution series of a plasmid standard carrying the target sequence from Chlamydia trachomatis and genomic DNA of this organism revealed that a single PCR-amplifiable target copy was sufficient to obtain a specific hybridization pattern.

TL;DR: Phylogenetic analysis of secY gene sequences resolved 10 genetically distinct lineages of Aster yellows group phytoplasmas and reinforced the notion that most subgroups identified by RFLP analysis ofsecY and rp gene sequences represent distinct phylogenetic lineages.

TL;DR: Overall, these results highlight the advantages of the MGB probe over the Taqman probe regarding mismatch discrimination, but suggest that optimization of reaction conditions and verification of the specificity are necessary also for MGB probes.

TL;DR: Primers for genus-specific PCR and for rapid discrimination of MCIV/DGIV/ISKNV and red sea bream iridovirus (RSIV), a notifiable pathogen, were developed were developed to determine that the prevalence of DGIV infection in diseased gourami in retail aquarium shops in Sydney was 22% (95% confidence limits 15-31%).

TL;DR: A multiplex reverse transcriptase-polymerase chain reaction (mRT-PCR) was developed and optimized for the detection of type A influenza virus; the assay simultaneously differentiates avian H5, H7 and H9 hemagglutinin subtypes.

TL;DR: The one-step RT-PCR approach proposed here is based on the synthesis of viroid-cDNA by reverse transcription at 60 degrees C using a viroid specific 27-mer primer followed by standard second strand synthesis plus PCR amplification with various primer pairs.

TL;DR: A nonisotopic Northern analysis method for miRNA detection using 3'-digoxigenin (DIG)-labeled RNA oligo probes that was equally sensitive compared to 32P-labeled probes in detecting miRNA quantities as low as 50 ng.

TL;DR: The aim of this study was to address the limitations of the widely used and commercially available Live/Dead BacLight Bacterial Viability kit (Molecular Probes, Eugene, OR), and a new combination of nucleic acid dyes, i.e. SYTO13 and SYTOX Orange, was proposed as an alternative.

TL;DR: The results showed marked variations in 18S rRNA, beta actin mRNA and GAPDH mRNA levels in mouse prostate explants and a human prostate cancer cell line following TSA treatment, and recommend use of RPL13A as a standard for normalization during TSA treatment.

TL;DR: Two species-specific PCR and oligonucleotide array assays were developed to detect the 16S-23S rDNA internal transcribed spacer of E. sakazakii and demonstrated that both of the pathogenic detections are time-saved and reliable.

TL;DR: The colonisation of the chicken gut by the two important pathogens Campylobacter jejuni and alpha-toxin gene containing Clostridium perfringens is compared using a new high-throughput automated DNA purification method for microbial biodiversity analyses.

TL;DR: A real-time reverse transcription multiplex polymerase chain reaction (rRT-MPCR) was developed for detection of mRNA encoded by rfbE and eae genes of enterohemorrhagic Escherichia coli (EHEC) O157:H7 and could be applied to rapid detection of very low levels of EHEC O157;H7 using total RNA as a template.

TL;DR: This work developed a multiplex PCR-RFLP protocols for the diagnosis of parasite genes associated with drug resistance, leading to significant decreases in reagent costs, time, number of manipulations and hence human resources.

TL;DR: This study utilised a 22,575 feature custom oligonucleotide DNA microarray designed from public domain databases of schistosome-expressed sequence tags to explore differential gene expression between the Philippine and Chinese strains of S. japonicum, and found that 593, 664 and 426 probes were differentially expressed between the two geographical strains.

TL;DR: Strain typing may help to better define the reservoir potential, carriership patterns, modes of transmission, and geographic distribution for each B. vinsonii berkhoffii type in future molecular epidemiological studies involving Bartonella infection in coyotes, dogs, gray foxes, human beings and potentially other animals or in arthropod vectors.

TL;DR: Investigation of the presence of viable MAP and MAP genetic components in cheese curds purchased from retail outlets in the northern and southern regions of Wisconsin and Minnesota found no viable MAP were able to be cultured.

TL;DR: This finding is indirect evidence that commercially available purified water can harbor low level contamination by L. pneumophila DNA that has escaped purification processes and presents a challenge when developing a sensitive DNA-based bacterial detection method.

TL;DR: This paper describes the development of a SYBR Green-based multiplex real time RT-PCR for the simultaneous detection of HCV and HIV-1 genomes in plasma samples, and indicates that the multiplex procedure detects at least 500 copies/ml of both HIV- 1 and HCV.

TL;DR: A DNA microarray chip of four virulence genes and 16S ribosomal DNA gene conserved region among all Gram negative species, including Yersinia, as a positive control was developed and evaluated and showed specificity of genotyping Y. enterocolitica using multiple microarray-based assays.

TL;DR: QIAamp and Puregene DNA extraction methods are well-suited for the preparation of paucicellular clinical samples for PCR-based assays and show the greatest dynamic range and the best linearity across the range of starting cell numbers.

TL;DR: The PCR-RFLP assay herein described may be useful to provide accurate, rapid and inexpensive identification of Perkinsus species, and may aid in ongoing epizooetiological studies and diseases control programmes.

TL;DR: A real-time PCR method to detect the presence of Shiga toxin producing E. coli O157:H7 was investigated and each of the three gene targets in one multiplex reaction could be distinguished by melt curve data with significantly different Tm's.

TL;DR: Four different primer combinations for conventional PCR, two non-competitive and two competitive set-ups for real time PCR were used for detection of Campylobacter spp.

TL;DR: The newly developed rapid test will essentially contribute to a better understanding of the mechanisms involved in the pathogenesis of FeLV infection and be especially useful in the development of antiretroviral vaccines and therapies aimed at the inhibition of proviral integration.

TL;DR: This is the first report describing the development of model DNA microarrays for determining the serogroup of E. coli strains using oligonucleotides and PCR products from genes in the O antigen gene clusters.

TL;DR: In this article, a real-time fluorogenic 5' nuclease PCR (TaqMan) was used to detect virus-vector trichodorid nematodes and associated Tobacco rattle virus (TRV).

TL;DR: This assay represents the first real-time PCR method capable of detecting C. trachomatis DNA and identifying serovar L-2 in the same reaction, directly from rectal swabs, and is reported here a rapid, sensitive, and specific real- time multiplex polymerase chain reaction (PCR) assay.

TL;DR: It is shown that the single tube real-time RT-PCR assay developed in this study can be applied as a rapid and sensitive method for specific detection of EV71 directly from clinical specimens.

TL;DR: It is demonstrated that low-density oligo microarray can serve as a reliable and time-saving method to HBV genotyping from patient's sera.

TL;DR: A rapid (<3h) and reliable assay for simultaneous detection of intestinal pathogens using two universal PCR primers to amplify two variable regions of bacterial 16S and 23S ribosomal DNA (rDNA) genes, and then applied to DNA microarrays, hybridization between probes and amplicons occurred.