Validation of the performance of a GMO multiplex screening assay based on microarray detection

A new screening method for the detection and identification of GMO, based on the use of multiplex PCR followed by microarray, has been developed and is presented. The technology is based on the identification of quite ubiquitous GMO genetic target elements first amplified by PCR, followed by direct hybridisation of the amplicons on a predefined microarray (DualChip^® GMO, Eppendorf, Germany). The validation was performed within the framework of a European project (Co-Extra, contract no 007158) and in collaboration with 12 laboratories specialised in GMO detection. The present study reports the strategy and the results of an ISO complying validation of the method carried out through an inter-laboratory study. Sets of blind samples were provided consisting of DNA reference materials covering all the elements detectable by specific probes present on the array. The GMO concentrations varied from 1% down to 0.045%. In addition, a mixture of two GMO events (0.1% RRS diluted in 100% TOPAS19/2) was incorporated in the study to test the robustness of the assay in extreme conditions. Data were processed according to ISO 5725 standard. The method was evaluated with predefined performance criteria with respect to the EC CRL method acceptance criteria. The overall method performance met the acceptance criteria; in particular, the results showed that the method is suitable for the detection of the different target elements at 0.1% concentration of GMO with a 95% accuracy rate. This collaborative trial showed that the method can be considered as fit for the purpose of screening with respect to its intra- and inter-laboratory accuracy. The results demonstrated the validity of combining multiplex PCR with array detection as provided by the DualChip^® GMO (Eppendorf, Germany) for the screening of GMO. The results showed that the technology is robust, practical and suitable as a screening tool.     

Raman studies of structural rearrangements induced in human plasma lipoprotein carotenoids by malondialdehyde

Raman and resonance Raman spectra of plasma lipoproteins ± malondialdehyde were studied at concentrations which block the normal receptor-mediated uptake by cells. The strong resonance Raman bands at about 1010, 1162 and 1530 cm⁻¹, due to the presence of carotenoids in the lipoproteins, are envisaged as structural probes. High resolution resonance Raman spectra of the 1500–1600 cm⁻¹ region reveal multiple features suggesting the coexistence of several structural populations of β-carotene whose precise assignment is complex. When plasma lipoproteins are reacted with malondialdehyde, a complex change occurs in the resonance Raman banding of β-carotene in the 1500–1600 cm⁻¹ region. Malonaldehyde (MDA) also modifies the acoustical region (70–200 cm⁻¹ of low density lipoprotein (LDL) lipids. We suggest that malondialdehyde association with plasma lipoproteins alters the lipid structure via apoprotein or apoprotein/lipid associations.     

Pollution source identification using a coupled diffusion model with a genetic algorithm

A new approach for the source quantification has been developed on the basis of real air pollutant hourly concentrations of SO₂, measured by three monitoring stations, during 9 h, around a group of three industrial sources. This inverse problem has been solved by coupling a direct model of diffusion (Pasquill’s Gaussian model) with a genetic algorithm, to search solutions leading to a minimum error between model outputs and measurements. The inversion performance depends on the relationship between the wind field and the configuration sources–receptors: good results are obtained when the monitoring stations are downwind from the sources, and in these cases, the order of magnitude of emissions is retrieved, sometimes with less than 10% error for at least two sources; there are some configurations (wind direction versus source and receptor locations) which do not permit to restore emissions. The latter situations reveal the need to conceive a specific network of sensors, taking into account the source locations and the most frequent weather patterns.     

N,N′-alkylated Imidazolium-Derivatives Act as Quorum-Sensing Inhibitors Targeting the Pectobacterium atrosepticum-Induced Symptoms on Potato Tubers

Bacteria belonging to the Pectobacterium genus are the causative agents of the blackleg and soft-rot diseases that affect potato plants and tubers worldwide. In Pectobacterium, the expression of the virulence genes is controlled by quorum-sensing (QS) and N-acylhomoserine lactones (AHLs). In this work, we screened a chemical library of QS-inhibitors (QSIs) and AHL-analogs to find novel QSIs targeting the virulence of Pectobacterium. Four N,N′-bisalkylated imidazolium salts were identified as QSIs; they were active at the μM range. In potato tuber assays, two of them were able to decrease the severity of the symptoms provoked by P. atrosepticum. This work extends the range of the QSIs acting on the Pectobacterium-induced soft-rot disease.     

Lipid oxidation products of heated soybeans as a possible cause of protection from ruminal biohydrogenation

Heating oilseeds has been shown to improve the milk fatty acid profile when given to dairy cows, compared to raw oilseeds. However, results from published studies are conflicting. The conditions of heating and storage of the oilseeds could be responsible for these differences, probably partly through their effects on lipid oxidation, the products of which could act on ruminal biohydrogenation (BH). Thus, 15 different treatments were applied to ground soybeans: three levels of heating (no heating, 30 min at 110 or 150°C) × 5 ambient storage durations (0, 1, 2, 4, or 6 months). Soybeans were incubated in vitro with ruminal fluid for 6 h. Triacylglycerol (TAG) polymers, hydroperoxides and hydroxyacids (HOA), aldehydes, and fatty acids were assayed in soybeans and ruminal culture. No TAG polymer was detected in any treatment. Soybeans stored for a long time had a high content of HOA, whereas those heated at 150°C, whatever the storage duration, had high aldehyde contents. The percentage disappearance of cis‐9,cis‐12 18:2 and cis‐9,cis‐12,cis‐15 18:3 in incubates decreased significantly in cultures with heated soybeans, especially at 150°C, suggesting that this partial protection of polyunsaturated fatty acids (PUFA) from BH was at least in part linked to the aldehyde content of the heated soybeans. Practical applications: Oilseeds given to ruminants are often heated, and heat treatment is known to generate oxidation products. Knowing what oxidation products influence ruminal biohydrogenation of unsaturated fatty acids could result in technological processes allowing a better transfer of unsaturated fatty acids from oilseeds to ruminant products.     

Design of poly(N‐acryloylglycine) materials for incorporation of microorganisms

To incorporate microorganisms and to preserve their integrity, new matrices of poly(N‐acryloylglycine) have been designed under appropriate conditions. To understand the interactions between the microorganisms and the organic part of the matrices, different conetworks of poly(N‐acryloylglycine) have been synthesized and characterized. Copolymerization with two crosslinkers was performed with different compositions. The thermal and swelling properties of conetworks are specifically controlled and compared. These investigations show that the swelling ratio of these materials is compatible with the incorporation of biomolecules in these matrices. They successfully permit Pseudomonasspecies 1625 bacteria incorporation. The biological activity of bacteria is also preserved, allowing the use of these materials for innovative biological applications. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 835‐841, 2013     

Mechanics-aided digital image correlation for the investigation of piezoelectric and ferroelectric behaviour of a soft PZT

The strain response of a polarised PZT was characterised using Digital Image Correlation (DIC). The DIC algorithm is based on a global approach and regularises the displacement field using the balance equations of solid mechanics. The measurement error is reduced by correcting the displacements that are mechanically not admissible. A ferroelectric test showed that the standard deviations of strain fields remain mostly under 1.2 × 10^?4 for an element size of 64 px. The standard deviation on the average value is 3 × 10^?6. The strain field is homogeneous and its average value is consistent with the strain obtained from a CCD laser measurement device. The longitudinal strain, transverse strain and polarisation response of the PZT were measured for bipolar and unipolar loadings ranging from 50 to 5000 V/mm. Material properties were extracted from these measurements. This work shows the advantages of a novel 2D-DIC algorithm for piezoelectric strain characterisation.     

Current transport in conducting particle filled epoxies

The electrical contact resistance between isolated pairs of micron-sized gold particles has been measured as a function of their separation using apparatus constructed in house. When incorporated into a percolation model for current transport in a conducting particle filled insulator, the results of such measurements have been shown to be consistent with the observed variation of conductivity with filler content beyond the percolation threshold in gold filled epoxies. This has been tested further by using adsorbed alkanethiol monolayers to control the interparticle spacing in the composites, demonstrating the importance of the contact resistance for the macroscopic current transport properties. Received: 22 September 1997/Revised version: 30 October 1997/Accepted: 31 October 1997     

Generating a Condensed Representation for Association Rules

Association rule extraction from operational datasets often produces several tens of thousands, and even millions, of association rules. Moreover, many of these rules are redundant and thus useless. Using a semantic based on the closure of the Galois connection, we define a condensed representation for association rules. This representation is characterized by frequent closed itemsets and their generators. It contains the non-redundant association rules having minimal antecedent and maximal consequent, called min-max association rules. We think that these rules are the most relevant since they are the most general non-redundant association rules. Furthermore, this representation is a basis, i.e., a generating set for all association rules, their supports and their confidences, and all of them can be retrieved needless accessing the data. We introduce algorithms for extracting this basis and for reconstructing all association rules. Results of experiments carried out on real datasets show the usefulness of this approach. In order to generate this basis when an algorithm for extracting frequent itemsets—such as Apriori for instance—is used, we also present an algorithm for deriving frequent closed itemsets and their generators from frequent itemsets without using the dataset.