New methods for the concentration of viruses from urban sewage using quantitative PCR.

Viruses are among the most important pathogens present in water contaminated with feces or urine and represent a serious risk to human health. Four procedures for concentrating viruses from sewage have been compared in this work, three of which were developed in the present study. Viruses were quantified using PCR techniques. According to statistical analysis and the sensitivity to detect human adenoviruses (HAdV), JC polyomaviruses (JCPyV) and noroviruses genogroup II (NoV GGII): (i) a new procedure (elution and skimmed-milk flocculation procedure (ESMP)) based on the elution of the viruses with glycine-alkaline buffer followed by organic flocculation with skimmed-milk was found to be the most efficient method when compared to (ii) ultrafiltration and glycine-alkaline elution, (iii) a lyophilization-based method and (iv) ultracentrifugation and glycine-alkaline elution. Through the analysis of replicate sewage samples, ESMP showed reproducible results with a coefficient of variation (CV) of 16% for HAdV, 12% for JCPyV and 17% for NoV GGII. Using spiked samples, the viral recoveries were estimated at 30-95% for HAdV, 55-90% for JCPyV and 45-50% for NoV GGII. ESMP was validated in a field study using twelve 24-h composite sewage samples collected in an urban sewage treatment plant in the North of Spain that reported 100% positive samples with mean values of HAdV, JCPyV and NoV GGII similar to those observed in other studies. Although all of the methods compared in this work yield consistently high values of virus detection and recovery in urban sewage, some require expensive laboratory equipment. ESMP is an effective low-cost procedure which allows a large number of samples to be processed simultaneously and is easily standardizable for its performance in a routine laboratory working in water monitoring. Moreover, in the present study, a CV was applied and proposed as a parameter to evaluate and compare the methods for detecting viruses in sewage samples.

New methods for the concentration of viruses from urban sewage using quantitative PCR.

Viruses are among the most important pathogens present in water contaminated with feces or urine and represent a serious risk to human health. Four procedures for concentrating viruses from sewage have been compared in this work, three of which were developed in the present study. Viruses were quantified using PCR techniques. According to statistical analysis and the sensitivity to detect human adenoviruses (HAdV), JC polyomaviruses (JCPyV) and noroviruses genogroup II (NoV GGII): (i) a new procedure (elution and skimmed-milk flocculation procedure (ESMP)) based on the elution of the viruses with glycine-alkaline buffer followed by organic flocculation with skimmed-milk was found to be the most efficient method when compared to (ii) ultrafiltration and glycine-alkaline elution, (iii) a lyophilization-based method and (iv) ultracentrifugation and glycine-alkaline elution. Through the analysis of replicate sewage samples, ESMP showed reproducible results with a coefficient of variation (CV) of 16% for HAdV, 12% for JCPyV and 17% for NoV GGII. Using spiked samples, the viral recoveries were estimated at 30-95% for HAdV, 55-90% for JCPyV and 45-50% for NoV GGII. ESMP was validated in a field study using twelve 24-h composite sewage samples collected in an urban sewage treatment plant in the North of Spain that reported 100% positive samples with mean values of HAdV, JCPyV and NoV GGII similar to those observed in other studies. Although all of the methods compared in this work yield consistently high values of virus detection and recovery in urban sewage, some require expensive laboratory equipment. ESMP is an effective low-cost procedure which allows a large number of samples to be processed simultaneously and is easily standardizable for its performance in a routine laboratory working in water monitoring. Moreover, in the present study, a CV was applied and proposed as a parameter to evaluate and compare the methods for detecting viruses in sewage samples.

MB-MDR: Model-Based Multifactor Dimensionality Reduction for detecting interactions in high-dimensional genomic data

L’anàlisi de l’efecte dels gens i els factors ambientals en el desenvolupament de malalties complexes és un gran repte estadístic i computacional. Entre les diverses metodologies de mineria de dades que s’han proposat per a l’anàlisi d’interaccions una de les més populars és el mètode Multifactor Dimensionality Reduction, MDR, (Ritchie i al. 2001). L’estratègia d’aquest mètode és reduir la dimensió multifactorial a u mitjançant l’agrupació dels diferents genotips en dos grups de risc: alt i baix. Tot i la seva utilitat demostrada, el mètode MDR té alguns inconvenients entre els quals l’agrupació excessiva de genotips pot fer que algunes interaccions importants no siguin detectades i que no permet ajustar per efectes principals ni per variables confusores. En aquest article il•lustrem les limitacions de l’estratègia MDR i d’altres aproximacions no paramètriques i demostrem la conveniència d’utilitzar metodologies parametriques per analitzar interaccions en estudis cas-control on es requereix l’ajust per variables confusores i per efectes principals. Proposem una nova metodologia, una versió paramètrica del mètode MDR, que anomenem Model-Based Multifactor Dimensionality Reduction (MB-MDR). La metodologia proposada té com a objectiu la identificació de genotips específics que estiguin associats a la malaltia i permet ajustar per efectes marginals i variables confusores. La nova metodologia s’il•lustra amb dades de l’Estudi Espanyol de Cancer de Bufeta.

Towards Detecting Changes in Underwater Image Sequences

Detecting changes between images of the same scene taken at different times is of great interest for monitoring and understanding the environment. It is widely used for on-land application but suffers from different constraints. Unfortunately, Change detection algorithms require highly accurate geometric and photometric registration. This requirement has precluded their use in underwater imagery in the past. In this paper, the change detection techniques available nowadays for on-land application were analyzed and a method to automatically detect the changes in sequences of underwater images is proposed. Target application scenarios are habitat restoration sites, or area monitoring after sudden impacts from hurricanes or ship groundings. The method is based on the creation of a 3D terrain model from one image sequence over an area of interest. This model allows for synthesizing textured views that correspond to the same viewpoints of a second image sequence. The generated views are photometrically matched and corrected against the corresponding frames from the second sequence. Standard change detection techniques are then applied to find areas of difference. Additionally, the paper shows that it is possible to detect false positives, resulting from non-rigid objects, by applying the same change detection method to the first sequence exclusively. The developed method was able to correctly find the changes between two challenging sequences of images from a coral reef taken one year apart and acquired with two different cameras

Development and application of a one-step low cost procedure to concentrate viruses from seawater samples

A novel and simple procedure for concentrating adenoviruses from seawater samples is described. The technique entails the adsorption of viruses to pre-flocculated skimmed milk proteins, allowing the flocs to sediment by gravity, and dissolving the separated sediment in phosphate buffer. Concentrated virus may be detected by PCR techniques following nucleic acid extraction. The method requires no specialized equipment other than that usually available in routine public health laboratories, and due to its straightforwardness it allows the processing of a larger number of water samples simultaneously. The usefulness of the method was demonstrated in concentration of virus in multiple seawater samples during a survey of adenoviruses in coastal waters.

A fully validated method for the determination of arsenic species in rice and infant cereal products

A full validation of inorganic arsenic (iAs), methylarsonic acid (MA), and dimethyl arsinic acid (DMA) in several types of rice and rice-based infant cereals is reported. The analytical method was developed and validated in two laboratories. The extraction of the As species was performed using nitric acid 0.2 % and hydrogen peroxide 1 %, and the coupled system liquid chromatography-inductively coupled plasma-mass spectrometry (LCICP-MS) was used for speciation measurements. Detection limit (DL), quantification limit, linearity, precision, trueness, accuracy, selectivity, as well as expanded uncertainty for iAs, MA, and DMA were established. The certified reference materials (CRMs) (NMIJ 7503a, NCS ZC73008, NIST SRM 1568a) were used to check the accuracy. The method was shown to be satisfactory in two proficiency tests (PTs). The broad applicability of the method is shown from the results of analysis of 29 samples including several types of rice, rice products, and infant cereal products. Total As ranged from 40.1 to 323.7 μg As kg1. From the speciation results, iAs was predominant, and DMA was detected in some samples while MA was not detected in any sample.

EMS mutagenesis in mature seed-derived rice calli as a new method for rapidly obtaining tilling mutant populations.

Background: TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetic method that combines chemical mutagenesis with high-throughput genome-wide screening for point mutation detection in genes of interest. However, this mutation discovery approach faces a particular problem which is how to obtain a mutant population with a sufficiently high mutation density. Furthermore, plant mutagenesis protocols require two successive generations (M1, M2) for mutation fixation to occur before the analysis of the genotype can begin. Results: Here, we describe a new TILLING approach for rice based on ethyl methanesulfonate (EMS) mutagenesis of mature seed-derived calli and direct screening of in vitro regenerated plants. A high mutagenesis rate was obtained (i.e. one mutation in every 451 Kb) when plants were screened for two senescence-related genes. Screening was carried out in 2400 individuals from a mutant population of 6912. Seven sense change mutations out of 15 point mutations were identified. Conclusions: This new strategy represents a significant advantage in terms of time-savings (i.e. more than eight months), greenhouse space and work during the generation of mutant plant populations. Furthermore, this effective chemical mutagenesis protocol ensures high mutagenesis rates thereby saving in waste removal costs and the total amount of mutagen needed thanks to the mutagenesis volume reduction.

Tourism Demand in Catalonia: detecting external economic factors

There is a lack of studies on tourism demand in Catalonia. To fill the gap, this paper focuses on detecting the macroeconomic factors that determine tourism demand in Catalonia. We also analyse the relation between these factors and tourism demand. Despite the strong seasonal component and the outliers in the time series of some countries, overnight stays give a better indication of tourism demand in Catalonia than the number of tourists. The degree of linear association between the macroeconomic variables and tourism demand is also higher when using quarterly rather than monthly data. Finally, there are notable differences between the results obtained for the different countries analysed. These results indicate that the best way to model tourism demand in Catalonia is to specify a quarterly model of overnight stays, differentiating between an aggregate demand model for the total number of tourists and specific models for each of the countries analysed.

Serological and virological surveys of the influenza A viruses in Antarctic and sub-Antarctic penguins

To evaluate the avian influenza virus (AIV) circulation in Antarctic and sub-Antarctic penguins we carried out a serosurvey on six species from Livingston, Marion and Gough islands. Seropositivity against AIV was performed on serum samples using a competitive enzyme-linked immunosorbent assay and haemagglutination and neuraminidase inhibition assays. Some oropharyngeal and cloacal swabs were also assayed to detect influenza virus genomes by real time reverse transcription-polymerase chain reaction. Overall, 12.1% (n = 140) penguins were seropositive to AIV. By species, we detected 5% (n = 19) and 11% (n = 18) seroprevalence in sub-Antarctic rockhopper penguins (Eudyptes spp.) from Gough and Marion islands, respectively, 42% (n = 33) seroprevalence in macaroni penguins (Eudyptes chysolophus Brandt), but no positives in the three other species, gentoo (Pygoscelis papua Forster; n = 25) and chinstrap penguins (P. antarctica Forster; n = 16), from Livingston Island and king penguins (Aptenodytes patagonicus Miller; n = 27) from Marion Island. While seropositivity reflected previous exposure to the AIV, the influenza genome was not detected. Our results indicate that AIV strains have circulated in penguin species in the sub-Antarctic region, but further studies are necessary to determine the precise role that such penguin species play in AIV epidemiology and if this circulation is species (or genus) specific.

Detecting Detection: International Perspectives on the Uses of a Plot

One of the problems with books which are relatively general in nature is that many of the individual contributions tend to be so narrow and specialised that only the author has any knowledge of (or interest in) the issues under discussion. At first sight this appears to be the case with Detecting Detection. Fortunately, however, first impressions are deceiving. Although the essays in the volume deal with writers as diverse and disparate as the Catalano-Spanish writer Juan Marse, the Bulgarian-French philosopher Julia Kristeva and the once-vaunted giant of English literature,Graham Greene, among numerous others, there is much to be enjoyed and learnt, even if some of the works under discussion are unfamiliar to the crime fiction reader and/or scholar to whom the book initially appears to be directed.

Approximate solution to the speed of spreading viruses

Recently, it has been shown that the speed of virus infections can be explained by time-delayed reactiondiffusion [J. Fort and V. Me´ndez, Phys. Rev. Lett. 89, 178101 (2002)], but no analytical solutions were found. Here we derive formulas for the front speed, valid in appropriate limits. We also integrate numerically the evolution equations of the system. There is good agreement with both numerical and experimental speeds

Time-Delayed Spread of Viruses in Growing Plaques

The spread of viruses in growing plaques predicted by classical models is greater than that measured experimentally. There is a widespread belief that this discrepancy is due to biological factors. Here we show that the observed speeds can be satisfactorily predicted by a purely physical model that takes into account the delay time due to virus reproduction inside infected cells. No free or adjustable parameters are used