PCR and real-time PCR primers developed for detection and identification of Bifidobacterium thermophilum in faeces

BACKGROUND: Culture-independent methods based on the 16S ribosomal RNA molecule are nowadays widely used for assessment of the composition of the intestinal microbiota, in relation to host health or probiotic efficacy. Because Bifidobacterium thermophilum was only recently isolated from human faeces until now, no specific real-time PCR (qPCR) assay has been developed for detection of this species as component of the bifidobacterial community of the human intestinal flora. RESULTS: Design of specific primers and probe was achieved based on comparison of 108 published bifidobacterial 16S rDNA sequences with the recently published sequence of the human faecal isolate B. thermophilum RBL67. Specificity of the primer was tested in silico by similarity search against the sequence database and confirmed experimentally by PCR amplification on 17 Bifidobacterium strains, representing 12 different species, and two Lactobacillus strains. The qPCR assay developed was linear for B. thermophilum RBL67 DNA quantities ranging from 0.02 ng/microl to 200 ng/microl and showed a detection limit of 10(5) cells per gram faeces. The application of this new qPCR assay allowed to detect the presence of B. thermophilum in one sample from a 6-month old breast-fed baby among 17 human faecal samples tested. Additionally, the specific qPCR primers in combination with selective plating experiments led to the isolation of F9K9, a faecal isolate from a 4-month old breast-fed baby. The 16S rDNA sequence of this isolate is 99.93% similar to that of B. thermophilum RBL67 and confirmed the applicability of the new qPCR assay in faecal samples. CONCLUSION: A new B. thermophilum-specific qPCR assay was developed based on species-specific target nucleotides in the 16S rDNA. It can be used to further characterize the composition of the bifidobacterial community in the human gastrointestinal tract. Until recently, B. thermophilum was considered as a species of animal origin, but here we confirm with the application of this new PCR assay the presence of B. thermophilum strains in the human gut.

Detection and landing behavior of emerald ash borer, Agrilus planipennis, at low population density

The exotic emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), was first discovered in North America in southeastern Michigan, USA, and Windsor, Ontario, Canada in 2002. Significant ash (Fraxinus spp.) mortality has been caused in areas where this insect has become well established, and new infestations continue to be discovered in several states in the United States and in Canada. This beetle is difficult to detect when it invades new areas or occurs at low density. Girdled trap tree and ground surveys have been important tools for detecting emerald ash borer populations, and more recently, purple baited prism traps have been used in detection efforts. Girdled trap trees were found to be more effective than purple prism traps at detecting emerald ash borer as they acted as sinks for larvae in an area of known low density emerald ash borer infestation. The canopy condition of the trap trees was not predictive of whether they were infested or not, indicating that ground surveys may not be effective for detection in an area of low density emerald ash borer population. When landing rates of low density emerald ash borer populations were monitored on non-girdled ash trees, landing rates were higher on larger, open grown trees with canopies that contain a few dead branches. As a result of these studies, we suggest that the threshold for emerald ash borer detection using baited purple prism traps hung at the canopy base of trees is higher than for girdled trap trees. In addition, detection of developing populations of EAB may be possible by selectively placing sticky trapping surfaces on non-girdled trap trees that are the larger and more open grown trees at a site.

Virus purification, detection and removal

The biopharmaceutical industry has a growing demand and an increasing need to improve the current virus purification technologies, especially as more and more vaccines are produced from cell-culture derived virus particles. Downstream purification strategies can be expensive and account for 70% of the overall manufacturing costs. The economic pressure and purification processes can be particularly challenging when the virus to be purified is small, as in our model virus, porcine parvovirus (PPV). Our efforts are focused on designing an easy, economical, scalable and efficient system for virus purification, and we focused on aqueous two-phase systems. Industry acceptable standards for virus vaccine recovery can be as low as 30% due to demand of high final titer, virus transduction inhibitors and presence of empty or defective virus capsids as impurities. We have overcome these shortcomings by recovering a high 64% of infectious virus using an aqueous two-phase system. We used high molecular weight polymer and citrate salt to achieve a good yield and eliminated the major contaminant bovine serum albumin. Viruses are also studied for ensuring pure and safe drinking water. Low pressure microfiltrations are continuously being investigated for water filters as they allow high permeate flux and low fouling. Viruses such as PPV are small enough to pass through the microporous membranes. Control of viruses in water is crucial for public health and we have designed an affinity based membrane filter to capture virus. Nanofibers have a high surface to volume ratio providing a highly accessible surface area for virus adsorption. Chitosan an insoluble, biocompatible and biodegradable polymer was used for adsorbing trimer peptide WRW. About 0.2 μmoles of cysteine terminal WRW peptide was conjugated to amine terminal chitosan using maleimide conjugation chemistry. We achieved 90-99% virus removal from water adjusted to a neutral pH. The virus removal from affinity based chitosan was attributed to electrostatic and hydrophobic driven binding effect.

EXPLORATION OF THE MTSAT2 SATELLITE CAPABILITIES FOR REAL TIME DETECTION AND CHARACTERIZATION OF VOLCANIC EMISSIONS

In this report, we attempt to define the capabilities of the infrared satellite remote sensor, Multifunctional Transport Satellite-2 (MTSAT-2) (i.e. a geosynchronous instrument), in characterizing volcanic eruptive behavior in the highly active region of Indonesia. Sulfur dioxide data from NASA's Ozone Monitoring Instrument (OMI) (i.e. a polar orbiting instrument) are presented here for validation of the processes interpreted using the thermal infrared datasets. Data provided from two case studies are analyzed specifically for eruptive products producing large thermal anomalies (i.e. lava flows, lava domes, etc.), volcanic ash and SO2 clouds; three distinctly characteristic and abundant volcanic emissions. Two primary methods used for detection of heat signatures are used and compared in this report including, single-channel thermal radiance (4-µm) and the normalized thermal index (NTI) algorithm. For automated purposes, fixed thresholds must be determined for these methods. A base minimum detection limit (MDL) for single-channel thermal radiance of 2.30E+05 Wm- 2sr-1m-1 and -0.925 for NTI generate false alarm rates of 35.78% and 34.16%, respectively. A spatial comparison method, developed here specifically for use in Indonesia and used as a second parameter for detection, is implemented to address the high false alarm rate. For the single-channel thermal radiance method, the utilization of the spatial comparison method eliminated 100% of the false alarms while maintaining every true anomaly. The NTI algorithm showed similar results with only 2 false alarms remaining. No definitive difference is observed between the two thermal detection methods for automated use; however, the single-channel thermal radiance method coupled with the SO2 mass abundance data can be used to interpret volcanic processes including the identification of lava dome activity at Sinabung as well as the mechanism for the dome emplacement (i.e. endogenous or exogenous). Only one technique, the brightness temperature difference (BTD) method, is used for the detection of ash. Trends of ash area, water/ice area, and their respective concentrations yield interpretations of increased ice formation, aggregation, and sedimentation processes that only a high-temporal resolution instrument like the MTSAT-2 can analyze. A conceptual model of a secondary zone of aggregation occurring in the migrating Kelut ash cloud, which decreases the distal fine-ash component and hazards to flight paths, is presented in this report. Unfortunately, SO2 data was unable to definitively reinforce the concept of a secondary zone of aggregation due to the lack of a sufficient temporal resolution. However, a detailed study of the Kelut SO2 cloud is used to determine that there was no climatic impacts generated from this eruption due to the atmospheric residence times and e-folding rate of ~14 days for the SO2. This report applies the complementary assets offered by utilizing a high-temporal and a high-spatial resolution satellite, and it demonstrates that these two instruments can provide unparalleled observations of dynamic volcanic processes.

A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex.

Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6-G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%). Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus.

IMILAST: A community effort to intercompare extratropical cyclone detection and tracking algorithms: assessing method-related uncertainties

The variability of results from different automated methods of detection and tracking of extratropical cyclones is assessed in order to identify uncertainties related to the choice of method. Fifteen international teams applied their own algorithms to the same dataset - the period 1989-2009 of interim European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERAInterim) data. This experiment is part of the community project Intercomparison of Mid Latitude Storm Diagnostics (IMILAST; see www.proclim.ch/imilast/index.html). The spread of results for cyclone frequency, intensity, life cycle, and track location is presented to illustrate the impact of using different methods. Globally, methods agree well for geographical distribution in large oceanic regions, interannual variability of cyclone numbers, geographical patterns of strong trends, and distribution shape for many life cycle characteristics. In contrast, the largest disparities exist for the total numbers of cyclones, the detection of weak cyclones, and distribution in some densely populated regions. Consistency between methods is better for strong cyclones than for shallow ones. Two case studies of relatively large, intense cyclones reveal that the identification of the most intense part of the life cycle of these events is robust between methods, but considerable differences exist during the development and the dissolution phases.

Detection and sequence analysis of a nickel-induced mutation in a retroviral model system

We have developed a novel way to assess the mutagenicity of environmentally important metal carcinogens, such as nickel, by creating a positive selection system based upon the conditional expression of a retroviral transforming gene. The target gene is the v-mos gene in MuSVts110, a murine retrovirus possessing a growth temperature dependent defect in expression of the transforming gene due to viral RNA splicing. In normal rat kidney cells infected with MuSVts110 (6m2 cells), splicing of the MuSVts110 RNA to form the mRNA from which the transforming protein, p85$\sp{\rm gag-mos}$, is translated is growth-temperature dependent, occurring at 33 C and below but not at 39 C and above. This splicing "defect" is mediated by cis-acting viral sequences. Nickel chloride treatment of 6m2 cells followed by growth at 39 C, allowed the selection of "revertant" cells which constitutively express p85$\sp{\rm gag-mos}$ due to stable changes in the viral RNA splicing phenotype, suggesting that nickel, a carcinogen whose mutagenicity has not been well established, could induce mutations in mammalian genes. We also show by direct sequencing of PCR-amplified integrated MuSVts110 DNA from a 6m2 nickel-revertant cell line that the nickel-induced mutation affecting the splicing phenotype is a cis-acting 70-base duplication of a region of the viral DNA surrounding the 3$\sp\prime$ splice site. These findings provide the first example of the molecular basis for a nickel-induced DNA lesion and establish the mutagenicity of this potent carcinogen. ^

Optimal dose levels in screening chest CT for unimpaired detection and volumetry of lung nodules, with and without computer assisted detection at minimal patient radiation

OBJECTIVES The aim of this phantom study was to minimize the radiation dose by finding the best combination of low tube current and low voltage that would result in accurate volume measurements when compared to standard CT imaging without significantly decreasing the sensitivity of detecting lung nodules both with and without the assistance of CAD. METHODS An anthropomorphic chest phantom containing artificial solid and ground glass nodules (GGNs, 5-12 mm) was examined with a 64-row multi-detector CT scanner with three tube currents of 100, 50 and 25 mAs in combination with three tube voltages of 120, 100 and 80 kVp. This resulted in eight different protocols that were then compared to standard CT sensitivity (100 mAs/120 kVp). For each protocol, at least 127 different nodules were scanned in 21-25 phantoms. The nodules were analyzed in two separate sessions by three independent, blinded radiologists and computer-aided detection (CAD) software. RESULTS The mean sensitivity of the radiologists for identifying solid lung nodules on a standard CT was 89.7% ± 4.9%. The sensitivity was not significantly impaired when the tube and current voltage were lowered at the same time, except at the lowest exposure level of 25 mAs/80 kVp [80.6% ± 4.3% (p = 0.031)]. Compared to the standard CT, the sensitivity for detecting GGNs was significantly lower at all dose levels when the voltage was 80 kVp; this result was independent of the tube current. The CAD significantly increased the radiologists' sensitivity for detecting solid nodules at all dose levels (5-11%). No significant volume measurement errors (VMEs) were documented for the radiologists or the CAD software at any dose level. CONCLUSIONS Our results suggest a CT protocol with 25 mAs and 100 kVp is optimal for detecting solid and ground glass nodules in lung cancer screening. The use of CAD software is highly recommended at all dose levels.

Active Testing for Face Detection and Localization

We provide a novel search technique which uses a hierarchical model and a mutual information gain heuristic to efficiently prune the search space when localizing faces in images. We show exponential gains in computation over traditional sliding window approaches, while keeping similar performance levels.