Padlock probes (PLPs) are long oligonucleotides, whose ends are complementary to adjacent target ... more Padlock probes (PLPs) are long oligonucleotides, whose ends are complementary to adjacent target sequences. Upon hybridization to the target, the two ends are brought into contact, allowing PLP circularization by ligation. PLPs provide extremely specific target recognition, which is followed by universal amplification and microarray detection. Since target recognition is separated from downstream processing, PLPs enable the development of flexible and extendable diagnostic systems, targeting diverse organisms. To adapt padlock technology for diagnostic purposes, we optimized PLP design to ensure high specificity and eliminating ligation on non-target sequences under real-world assay conditions. We designed and tested 11 PLPs to target various plant pathogens at the genus, species and subspecies levels, and developed a prototype PLP-based plant health chip. Excellent specificity was demonstrated toward the target organisms. Assay background was determined for each hybridization using a no-target reference sample, which provided reliable and sensitive identification of positive samples. A sensitivity of 5 pg genomic DNA and a dynamic range of detection of 100 were observed. The developed multiplex diagnostic system was validated using genomic DNAs of characterized isolates and artificial mixtures thereof. The demonstrated system is adaptable to a wide variety of applications ranging from pest management to environmental microbiology.
An RT-PCR/nested PCR technique was developed for the simultaneous detection and typing of plum po... more An RT-PCR/nested PCR technique was developed for the simultaneous detection and typing of plum pox virus (PPV) and its major types--Dideron (D), Marcus (M), El-Amar (EA) and Cherry (C). Degenerated oligonucleotides were synthesized for the general detection of PPV, flanking the coding sequence for the N-terminal portion of the coat protein (CP), within which strain-specific differences were identified. On the basis of these characteristic differences, degenerated primer pairs were designed to differentiate between the four major subgroups of the virus in nested PCR reactions. The validity of the technique was tested on viral strains and cloned cDNAs overlapping the CP region. High specificity was observed with no detectable cross-reactions. The results of general PPV detection with the new primers and those of the PCR-based detection of the 3' non-coding region of the viral genome correlated with complete coincidence. The PCR typing results correlated well with those of the RsaI-RFLP and serological typing and revealed a surprisingly high incidence of PPV-D in Hungary.
A multiplex AmpliDet RNA assay was developed for the specific detection of potato virus Y (PVY), ... more A multiplex AmpliDet RNA assay was developed for the specific detection of potato virus Y (PVY), and for the differentiation of the PVY(N), PVY(O/C) strains and the tuber necrotic isolates (PVY(NTN)). The assay is based on the generic amplification of a region within the coat protein coding region of all known PVY isolates by nucleic acid sequence-based amplification (NASBA) and strain-specific detection by molecular beacons. PVY(NTN)-specific diagnosis is achieved by detecting PVY(N) and PVY(O)-specific sequences flanking a recombination site that is associated with the tuber necrotic pathotype. The assay exhibited good specificity toward the various PVY strains in both single and mixed infections. The technique was validated by the use of 47 PVY isolates originating from six countries. The results of the AmpliDet RNA assay were identical or consistent with those of biological characterisation in the decisive majority of cases.
Galectin-1 (Gal-1) is an endogenous mammalian S-type lectin with highly pleiotropic effect on dif... more Galectin-1 (Gal-1) is an endogenous mammalian S-type lectin with highly pleiotropic effect on different tissues. The viability of the lymphoid cells is reduced by gal-1 by triggering apoptosis, however, the mechanism of the gal-1 induced apoptosis is still under investigation. The receptor tyrosine phosphatase, CD45, a heavily glycosylated cell surface molecule binds to gal-1 with high affinity, however, its contribution to the gal-1 induced apoptosis is still controversial. In this study we show that galectin-1 binds to cells deficient for CD45, although CD45 is one of the galectin-1-binding cell surface proteins on T cells. Moreover, the CD45 deficient Jurkat variant, J45.01 responds readily with tyrosine phosphorylation and subsequent apoptosis to galectin-1 treatment in a similar degree as its wild type counterpart, Jurkat does. These results strongly indicate that CD45 is not the receptor via gal-1 mediates the apoptotic signal into the cells as it was suggested in previous studies.
An overview is given of rapid methods for the detection of plant-related organisms in plant mater... more An overview is given of rapid methods for the detection of plant-related organisms in plant material, soil, compost, water, etc. Protein-based detection assays such as isozyme analysis, ELISA, immunofluorescence colony-staining and future applications of immunological tests are described as well as nucleic acid-based tests. Examples of RNA amplification tests, such as RT-PCR, NASBA and AmpliDet RNA are given, and numerous DNA-based tests using PCR, either with or without the use of probes, are illustrated. Most tests described are directed towards the detection of plant pathogens such as viruses, bacteria, fungi and nematodes. A test for the detection of mRNA of a mycotoxin producing fungus is also shown in this review. This illustrates that the technology of many of the tests described can equally well be used for the development of assays to detect harmful organisms in food, feed, water, air or any other environment in the agrofood production chain. The latest development in detection are in the field of multiplex detection using microarrays is presented as the pUMA technology.
Simultaneous detection and identification of multiple pathogenic microorganisms in complex enviro... more Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, backgroundfree ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5 and 3 ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10 4 . A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.
Padlock probes (PLPs) are long oligonucleotides, whose ends are complementary to adjacent target ... more Padlock probes (PLPs) are long oligonucleotides, whose ends are complementary to adjacent target sequences. Upon hybridization to the target, the two ends are brought into contact, allowing PLP circularization by ligation. PLPs provide extremely specific target recognition, which is followed by universal amplification and microarray detection. Since target recognition is separated from downstream processing, PLPs enable the development of flexible and extendable diagnostic systems, targeting diverse organisms. To adapt padlock technology for diagnostic purposes, we optimized PLP design to ensure high specificity and eliminating ligation on non-target sequences under real-world assay conditions. We designed and tested 11 PLPs to target various plant pathogens at the genus, species and subspecies levels, and developed a prototype PLP-based plant health chip. Excellent specificity was demonstrated toward the target organisms. Assay background was determined for each hybridization using a no-target reference sample, which provided reliable and sensitive identification of positive samples. A sensitivity of 5 pg genomic DNA and a dynamic range of detection of 100 were observed. The developed multiplex diagnostic system was validated using genomic DNAs of characterized isolates and artificial mixtures thereof. The demonstrated system is adaptable to a wide variety of applications ranging from pest management to environmental microbiology.
An RT-PCR/nested PCR technique was developed for the simultaneous detection and typing of plum po... more An RT-PCR/nested PCR technique was developed for the simultaneous detection and typing of plum pox virus (PPV) and its major types--Dideron (D), Marcus (M), El-Amar (EA) and Cherry (C). Degenerated oligonucleotides were synthesized for the general detection of PPV, flanking the coding sequence for the N-terminal portion of the coat protein (CP), within which strain-specific differences were identified. On the basis of these characteristic differences, degenerated primer pairs were designed to differentiate between the four major subgroups of the virus in nested PCR reactions. The validity of the technique was tested on viral strains and cloned cDNAs overlapping the CP region. High specificity was observed with no detectable cross-reactions. The results of general PPV detection with the new primers and those of the PCR-based detection of the 3' non-coding region of the viral genome correlated with complete coincidence. The PCR typing results correlated well with those of the RsaI-RFLP and serological typing and revealed a surprisingly high incidence of PPV-D in Hungary.
A multiplex AmpliDet RNA assay was developed for the specific detection of potato virus Y (PVY), ... more A multiplex AmpliDet RNA assay was developed for the specific detection of potato virus Y (PVY), and for the differentiation of the PVY(N), PVY(O/C) strains and the tuber necrotic isolates (PVY(NTN)). The assay is based on the generic amplification of a region within the coat protein coding region of all known PVY isolates by nucleic acid sequence-based amplification (NASBA) and strain-specific detection by molecular beacons. PVY(NTN)-specific diagnosis is achieved by detecting PVY(N) and PVY(O)-specific sequences flanking a recombination site that is associated with the tuber necrotic pathotype. The assay exhibited good specificity toward the various PVY strains in both single and mixed infections. The technique was validated by the use of 47 PVY isolates originating from six countries. The results of the AmpliDet RNA assay were identical or consistent with those of biological characterisation in the decisive majority of cases.
Galectin-1 (Gal-1) is an endogenous mammalian S-type lectin with highly pleiotropic effect on dif... more Galectin-1 (Gal-1) is an endogenous mammalian S-type lectin with highly pleiotropic effect on different tissues. The viability of the lymphoid cells is reduced by gal-1 by triggering apoptosis, however, the mechanism of the gal-1 induced apoptosis is still under investigation. The receptor tyrosine phosphatase, CD45, a heavily glycosylated cell surface molecule binds to gal-1 with high affinity, however, its contribution to the gal-1 induced apoptosis is still controversial. In this study we show that galectin-1 binds to cells deficient for CD45, although CD45 is one of the galectin-1-binding cell surface proteins on T cells. Moreover, the CD45 deficient Jurkat variant, J45.01 responds readily with tyrosine phosphorylation and subsequent apoptosis to galectin-1 treatment in a similar degree as its wild type counterpart, Jurkat does. These results strongly indicate that CD45 is not the receptor via gal-1 mediates the apoptotic signal into the cells as it was suggested in previous studies.
An overview is given of rapid methods for the detection of plant-related organisms in plant mater... more An overview is given of rapid methods for the detection of plant-related organisms in plant material, soil, compost, water, etc. Protein-based detection assays such as isozyme analysis, ELISA, immunofluorescence colony-staining and future applications of immunological tests are described as well as nucleic acid-based tests. Examples of RNA amplification tests, such as RT-PCR, NASBA and AmpliDet RNA are given, and numerous DNA-based tests using PCR, either with or without the use of probes, are illustrated. Most tests described are directed towards the detection of plant pathogens such as viruses, bacteria, fungi and nematodes. A test for the detection of mRNA of a mycotoxin producing fungus is also shown in this review. This illustrates that the technology of many of the tests described can equally well be used for the development of assays to detect harmful organisms in food, feed, water, air or any other environment in the agrofood production chain. The latest development in detection are in the field of multiplex detection using microarrays is presented as the pUMA technology.
Simultaneous detection and identification of multiple pathogenic microorganisms in complex enviro... more Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, backgroundfree ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5 and 3 ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10 4 . A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.
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Papers by M. Szemes