Biomedical subjects

Maria Pla

Publications and source records attributed to Maria Pla.

26 records · Page 2Linked to original sources

PubMed2004

Construction strategy for an internal amplification control for real-time diagnostic assays using nucleic Acid sequence-based amplification: development and clinical application.

An important analytical control in molecular amplification-based methods is an internal amplification control (IAC), which should be included in each reaction mixture. An IAC is a nontarget nucleic acid sequence which is coamplified simultaneously with the target sequence. With negative results for the target nucleic acid, the absence of an IAC signal indicates that amplification has failed. A general strategy for the construction of an IAC for inclusion in molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assays is presented. Construction proceeds in two phases. In the first phase, a double-stranded DNA molecule that contains nontarget sequences flanked by target sequences complementary to the NASBA primers is produced. At the 5' end of this DNA molecule is a T7 RNA polymerase binding sequence. In the second phase of construction, RNA transcripts are produced from the DNA by T7 RNA polymerase. This RNA is the IAC; it is amplified by the target NASBA primers and is detected by a molecular beacon probe complementary to the internal nontarget sequences. As a practical example, an IAC for use in an assay for the detection of Mycobacterium avium subsp. paratuberculosis is described, its incorporation and optimization within the assay are detailed, and its application to spiked and natural clinical samples is shown to illustrate the correct interpretation of the diagnostic results.

Animals↗

PubMed2003

Development of melting temperature-based SYBR Green I polymerase chain reaction methods for multiplex genetically modified organism detection.

Commercialization of several genetically modified crops has been approved worldwide to date. Uniplex polymerase chain reaction (PCR)-based methods to identify these different insertion events have been developed, but their use in the analysis of all commercially available genetically modified organisms (GMOs) is becoming progressively insufficient. These methods require a large number of assays to detect all possible GMOs present in the sample and thereby the development of multiplex PCR systems using combined probes and primers targeted to sequences specific to various GMOs is needed for detection of this increasing number of GMOs. Here we report on the development of a multiplex real-time PCR suitable for multiple GMO identification, based on the intercalating dye SYBR Green I and the analysis of the melting curves of the amplified products. Using this method, different amplification products specific for Maximizer 176, Bt11, MON810, and GA21 maize and for GTS 40-3-2 soybean were obtained and identified by their specific Tm. We have combined amplification of these products in a number of multiplex reactions and show the suitability of the methods for identification of GMOs with a sensitivity of 0.1% in duplex reactions. The described methods offer an economic and simple alternative to real-time PCR systems based on sequence-specific probes (i.e., TaqMan chemistry). These methods can be used as selection tests and further optimized for uniplex GMO quantification.

Benzothiazoles↗

PubMed2003

A 10-kDa class-CI sHsp protects E. coli from oxidative and high-temperature stress.

We report on a new cDNA clone (Qshsp10.4-CI) of a Quercus suber L. class-CI small heat-shock protein (sHsp) obtained from cork (phellem), a highly oxidatively stressed plant tissue. The deduced gene product lacks the C-terminal extension and the consensus I region of the alpha-crystallin domain, being the most C-terminally truncated sHsp reported to date. In an attempt to prove that a protective function is possible for such a truncated sHsp, we overexpressed in Escherichia coli three recombinant sHsp-CIs, one (rQsHsp10.4-CI) showing the same truncation as Qshsp10.4-CI, a second (rN49) lacking the whole alpha-crystallin domain, and a third (rN153) consisting of a full-length sHsp-CI. The overexpression of rN153 and, remarkably, rQsHsp10.4-CI but not rN49 enhanced cell viability under high temperature and, interestingly, under oxidative stress. These results show that the C-terminal extension and the consensus I region of the alpha-crystallin domain are dispensable, but amino acids 1-41 of the alpha-crystallin domain (including the consensus II region) are essential for the protective activity of sHsp-CIs. On the other hand, two-dimensional immunodetection patterns showed accumulation of ca. 10-kDa sHsp-CI immunorelated polypeptides in cork and other oxidatively stressed tissues but not in control and heat-stressed tissues. We discuss the possible role of highly truncated sHsps in relation to oxidative stress.

Amino Acid Sequence↗

PubMed2003

A rapid and direct real time PCR-based method for identification of Salmonella spp.

The aim of this work was the validation of a rapid, real-time PCR assay based on TaqMan technology for the unequivocal identification of Salmonella spp. to be used directly on an agar-grown colony. A real-time PCR system targeting at the Salmonella spp. invA gene was optimized and validated through a four times repeated blind experiment performed in two different laboratories including 50 Salmonella spp. with representative strains from each of the 5 different Salmonella subgenera and 30 non-Salmonella strains. Both parameters DeltaR(n) (fluorescence intensity of template through a normalized reporter value) and C(T) (cycle at which the fluorescence intensity achieved a pre-established threshold) were analyzed. Overall mean DeltaR(n) and C(T) values for Salmonella strains (2.14+/-0.87 and 15.30+/-0.90, respectively) were statistically different from values for non-Salmonella strains, allowing the establishment of cut-off DeltaR(n) and C(T) values based on 95% confidence intervals that allowed the correct identification of all strains tested in each independent experiment. The accuracy of this assay in terms of inclusivity and exclusivity was 100%. Moreover, the PCR system proved to be especially convenient because the pre-mix containing all PCR reagents except for the bacterial cells could be kept at -20 degrees C for at least 1 month before its use. The optimized TaqMan real-time PCR assay is a useful, simple and rapid method for routine identification of Salmonella spp., irrespective of the particular subgenus.

Bacterial Proteins↗

PubMed2003

A specific real-time quantitative PCR detection system for event MON810 in maize YieldGard based on the 3'-transgene integration sequence.

The increasing presence of transgenic plant derivatives in a wide range of animal and human consumables has provoked in western Europe a strong demand for appropriate detection methods to evaluate the existence of transgenic elements. Among the different techniques currently used, the real-time quantitative PCR is a powerful technology well adapted to the mandatory labeling requirements in the European Union (EU). The use of transgene flanking genomic sequences has recently been suggested as a means to avoid ambiguous results both in qualitative and quantitative PCR-based technologies. In this study we report the identification of genomic sequences adjacent to the 3'-integration site of event MON810 in transgenic maize. This genetically modified crop contains transgene sequences leading to ectopic expression of a synthetic CryIA(b) endotoxin which confers resistance to lepidopteran insects especially against the European corn borer. The characterization of the genome-transgene junction sequences by means of TAIL-PCR has facilitated the design of a specific, sensitive and accurate quantification method based on TaqMan chemistry. Cloning of event MON810 3'-junction region has also allowed to compare the suitability of plasmid target sequences versus genomic DNA obtained from certified reference materials (CRMs), to prepare standard calibration curves for quantification.

Animals↗

PubMed2003

Real-time and conventional polymerase chain reaction systems based on the metallo-carboxypeptidase inhibitor gene for specific detection and quantification of potato and tomato in processed food.

In this paper, a method for the specific detection and quantification of potato and tomato DNA in food samples with the use of conventional and real-time polymerase chain reaction (PCR) is described. This method is adequate for use in food quality routine assays involving highly processed samples for which very tiny amounts of DNA are expected. Detection was achieved by amplifying a region of the metallo-carboxypeptidase inhibitor gene from either the potato (PCI) or the tomato (MCPI) and by using specific primers complementary to the propeptide regions of these inhibitors, which were found to differ for the potato and tomato proproteins. Conventional and real-time PCR systems were based on the same potato- or tomato-specific primer pairs, and quantification was carried out with a TaqMan chemistry-based probe. The methods developed proved to be very specific and sensitive and highly reliable for the identification and quantification of DNA from both plant species. In addition, the construction of plasmids pPAT and pTOM, suitable for use as external calibration standards for the elaboration of comparative amplification profiles, is reported. Limits of detection and quantification with the use of these plasmid standards are given. Specificity and copy number conservation among different cultivars were analyzed, and the reliability of these systems was tested through their application to the analysis of commercial food samples including potato and/or tomato as components.

Base Sequence↗

PubMed2002

Developmentally and stress-induced small heat shock proteins in cork oak somatic embryos.

The timing and tissue localization of small heat shock proteins (sHSPs) during cork oak somatic embryo development was investigated under normal growing culture conditions and in response to stress. Western blot analyses using polyclonal antibodies raised against cork oak recombinant HSP17 showed a transient accumulation of class I sHSPs during somatic embryo maturation and germination. Moreover, the amount of protein increased at all stages of embryo development in response to exogenous stress. The developmentally accumulated proteins localized to early differentiating, but not the highly dividing, regions of the root and shoot apical meristems. By contrast, these highly dividing regions were strongly immunostained after heat stress. Findings support the hypothesis of a distinct control for developmentally and stress-induced accumulation of class I sHSPs. The possible role of sHSPs is discussed in relation to their tissue specific localization.

Adaptation, Physiological↗

PubMedDate not supplied

Interlaboratory transfer of a real-time polymerase chain reaction assay for quantitative detection of genetically modified maize event TC-1507.

A real-time polymerase chain reaction (QPCR) assay was developed for quantitative detection of a genetically modified (GM) maize event TC-1507 and modification to conventional PCR for qualitative purposes. Sequences 5'-flanking TC-1507 full-length insert were characterized and showed multiple rearrangements involving insert and maize chloroplast fragments. The event specificity of the TC-1507 assays was based on the detection of transgene and plant rearranged sequences found to 5' flank the insertion site. They were fully specific and exhibited a limit of detection below 10 target copies, allowing consistent detection of 0.1% GM levels. The QPCR was highly linear and efficient and proved adequate for quantification of GM contents, aiming at the fulfillment of legal requirements established in the European Union (i.e., compulsory labeling of TC-1507 levels >0.9%). It satisfactorily determined TC-1507 contents on different matrixes and was successfully transferred a different laboratory.

Base Sequence↗