Identification of Trypanosomatids by detecting Single Nucleotide Fingerprints using DNA analysis by dynamic chemistry with MALDI-ToF

Luque-González, María Angélica; Tabraue-Chávez, Mavys; López‐Longarela, Bárbara; Sánchez‐Martín, Rosario M.; Ortiz-González, Matilde; Soriano, Miguel; García‐Salcedo, José A.; Pernagallo, Salvatore; Díaz‐Mochón, Juan José

doi:10.1016/j.talanta.2017.07.059

Cited by 20 publications

(17 citation statements)

References 31 publications

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“…While our previous mass spectrometry method 29 allowed parasite species detection and characterization by measurement of molecular weight differences between abasic PNA probes and aldehyde-modified nucleobases (SMART-Bases), in this Spin-Tube platform it was required that the SMART-Base were biotin-labelled (Figs S3–S5 in SI) 41,42 . Here the color development reaction depends on the biotin recognition by a streptavidin-alkaline phosphatase complex, that transforms a colorless chromogenic substrate (NBT/BCIP, nitro blue tetrazolium chloride/5-Bromo-4-chloro-3-indolyl phosphate) into a blue precipitate each time there is a biotin tag attached to the membrane.…”

Section: Resultsmentioning

confidence: 99%

“…Besides the tests available today 19,26 , our group has recently reported the successful detection and differentiation of three Trypanosomatids species, by detecting Single Nucleotide Fingerprint (SNF) markers using a dynamic chemical approach for nucleic acid reading (ChemNAT technology) 27,28 in combination with MALDI-ToF 29 . SNF markers are single nucleotide variations that occur at specific positions in conserved target nucleic acid sequences, allowing the differentiation of pathogenic species.…”

Section: Introductionmentioning

confidence: 99%

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A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species

Tabraue-Chávez

Luque-González

Marín-Romero

et al. 2019

Sci Rep

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Leishmaniasis and Chagas disease are endemic in many countries, and re-emerging in the developed countries. A rapid and accurate diagnosis is important for early treatment for reducing the duration of infection as well as for preventing further potential health complications. In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi . The assay consists of a singleplex PCR step that amplifies a highly homologous DNA sequence which encodes for the RNA component of the large ribosome subunit. The amplicons of the two different parasites differ between them by single nucleotide variations, known as “Single Nucleotide Fingerprint” (SNF) markers. The SNF markers can be easily identified by naked eye using a novel micro Spin-Tube device "Spin-Tube", as each of them creates a specific spot pattern. Moreover, the direct use of ribosomal RNA without requiring the PCR pre-amplification step is also feasible, further increasing the simplicity of the assay. The molecular assay delivers sensitivity capable of identifying up to 8.7 copies per µL with single mismatch specificity. The Spin-Tube thus represents an innovative solution providing benefits in terms of time, cost, and simplicity, all of which are crucial for the diagnosis of infectious disease in developing countries.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species

Tabraue-Chávez

Luque-González

Marín-Romero

et al. 2019

Sci Rep

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“…With the advances made by our team with dynamic chemical labelling (DCL) technology for the direct detection of nucleic acids, the deliverable of simultaneous detection of protein and miRNA in clinical samples is now possible. The DCL approach [17][18][19][20][27][28][29][30][31][32][33] is particularly well suited to deliver consistent and reliable quantitative readings of miRNAs in clinical samples when merged with bead-based systems. By simplifying the workflow, especially removing extraction, isolation and amplification steps, DCL was able to direct detect miRNAs in enzyme-linked immunosorbent assay (ELISA)-type format without affecting protein co-analytes, overcoming the current limitation issues that inhibit the development of simultaneous detection of proteins and miRNAs with high specificity and accuracy.…”

Section: Introductionmentioning

confidence: 99%

Simultaneous Detection of Drug-Induced Liver Injury Protein and microRNA Biomarkers Using Dynamic Chemical Labelling on a Luminex MAGPIX System

et al. 2021

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Drug-induced liver injury (DILI) is a potentially fatal adverse event and a leading cause for pre- and post-marketing drug withdrawal. Several multinational DILI initiatives have now recommended a panel of protein and microRNA (miRNA) biomarkers that can detect early liver injury and inform about mechanistic basis. This manuscript describes the development of seqCOMBO, a unique combo-multiplexed assay which combines the dynamic chemical labelling approach and an antibody-dependant method on the Luminex MAGPIX system. SeqCOMBO enables a versatile multiplexing platform to perform qualitative and quantitative analysis of proteins and miRNAs in patient serum samples simultaneously. To the best of our knowledge, this is the first method to profile protein and miRNA biomarkers to diagnose DILI in a single-step assay.

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“…In addition, DNA analysis has also been applied in identifying pork, beef, chicken and mutton origins in food products [ 5 ] and feed products [ 6 , 7 ] to control adulteration. Besides, it has contributed to the identification of parasite for the rapid detection of infectious disease [ 8 ]. In general, methods for the identification of DNA, such as polymerase chain reaction (PCR), DNA metabarcoding, and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) have been commonly used in these studies.…”

Section: Introductionmentioning

confidence: 99%

Insight into Rapid DNA-Specific Identification of Animal Origin Based on FTIR Analysis: A Case Study

et al. 2018

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In this study, a methodology has been proposed to identify the origin of animal DNA, employing high throughput extension accessory Fourier transform infrared (HT-FTIR) spectroscopy coupled with chemometrics. Important discriminatory characteristics were identified in the FTIR spectral peaks of 51 standard DNA samples (25 from bovine and 26 from fish origins), including 1710, 1659, 1608, 1531, 1404, 1375, 1248, 1091, 1060, and 966 cm−1. In particular, the bands at 1708 and 1668 cm−1 were higher in fish DNA than in bovine DNA, while the reverse was true for the band at 1530 cm−1 was shown the opposite result. It was also found that the PO2− Vas/Vs ratio (1238/1094 cm−1) was significantly higher (p < 0.05) in bovine DNA than in fish DNA. These discriminatory characteristics were further revealed to be closely related to the base content and base sequences of different samples. Multivariate analyses, such as principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were conducted, and both the sensitivity and specificity values of PLS-DA model were one. This methodology has been further validated by 20 meat tissue samples (4 from bovine, 5 from ovine, 5 from porcine, and 6 from fish origins), and these were successfully differentiated. This case study demonstrated that FTIR spectroscopy coupled with PLS-DA discriminant model could provide a rapid, sensitive, and reliable approach for the identification of DNA of animal origin. This methodology could be widely applied in food, feed, forensic science, and archaeology studies.

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Identification of Trypanosomatids by detecting Single Nucleotide Fingerprints using DNA analysis by dynamic chemistry with MALDI-ToF

Cited by 20 publications

References 31 publications

A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species

A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species

Simultaneous Detection of Drug-Induced Liver Injury Protein and microRNA Biomarkers Using Dynamic Chemical Labelling on a Luminex MAGPIX System

Insight into Rapid DNA-Specific Identification of Animal Origin Based on FTIR Analysis: A Case Study

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