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Your search keyword '"Dunja Urbančič"' showing total 3 results
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3 results on '"Dunja Urbančič"'

1. Robust Saliva-Based RNA Extraction-Free One-Step Nucleic Acid Amplification Test for Mass SARS-CoV-2 Monitoring

Author

Eva Rajh, Tina Šket, Arne Praznik, Petra Sušjan, Alenka Šmid, Dunja Urbančič, Irena Mlinarič-Raščan, Polona Kogovšek, Tina Demšar, Mojca Milavec, Katarina Prosenc Trilar, Žiga Jensterle, Mihaela Zidarn, Viktorija Tomič, Gabriele Turel, Tatjana Lejko-Zupanc, Roman Jerala, and Mojca Benčina

Subjects
saliva, COVID-19, SARS-CoV-2, LAMP, RT-qPCR, passive drool, Organic chemistry, QD241-441
Abstract

Early diagnosis with rapid detection of the virus plays a key role in preventing the spread of infection and in treating patients effectively. In order to address the need for a straightforward detection of SARS-CoV-2 infection and assessment of viral spread, we developed rapid, sensitive, extraction-free one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) tests for detecting SARS-CoV-2 in saliva. We analyzed over 700 matched pairs of saliva and nasopharyngeal swab (NSB) specimens from asymptomatic and symptomatic individuals. Saliva, as either an oral cavity swab or passive drool, was collected in an RNA stabilization buffer. The stabilized saliva specimens were heat-treated and directly analyzed without RNA extraction. The diagnostic sensitivity of saliva-based RT-qPCR was at least 95% in individuals with subclinical infection and outperformed RT-LAMP, which had at least 70% sensitivity when compared to NSBs analyzed with a clinical RT-qPCR test. The diagnostic sensitivity for passive drool saliva was higher than that of oral cavity swab specimens (95% and 87%, respectively). A rapid, sensitive one-step extraction-free RT-qPCR test for detecting SARS-CoV-2 in passive drool saliva is operationally simple and can be easily implemented using existing testing sites, thus allowing high-throughput, rapid, and repeated testing of large populations. Furthermore, saliva testing is adequate to detect individuals in an asymptomatic screening program and can help improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

Published
2021
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2. Methylation of selenocysteine catalysed by thiopurine S-methyltransferase

Author

Irena Mlinarič-Raščan, Alenka Šmid, Janez Plavec, Anita Kotar, Marko Jukič, Stanislav Gobec, Lars-Göran Mårtensson, and Dunja Urbančič

Subjects
Magnetic Resonance Spectroscopy, Binding analysis, enzymatic methylation, NMR spectroscopy, S-adenosylmethionine, selenocysteine thiopurine, S-methyltransferase, Molecular Conformation, 01 natural sciences, Biochemistry, chemistry.chemical_compound, Catalytic Domain, chemistry.chemical_classification, 0303 health sciences, biology, Thiopurine methyltransferase, Selenocysteine, Chemistry, S-metiltransferaze, Nuclear magnetic resonance spectroscopy, Methylation, Recombinant Proteins, Amino acid, Molecular Docking Simulation, udc:543.2/.9, binding analysis, Jedrska magnetna resonanca, Protein Binding, selenocysteine, Biophysics, Catalysis, 03 medical and health sciences, Thiopurine S-Methyltransferase, Selenium, NMR spectroscopy, Humans, analizne metode, udc:543.429.23:615, Molecular Biology, 030304 developmental biology, S-adenosylmethionine, 010405 organic chemistry, Tryptophan, Active site, Methyltransferases, 0104 chemical sciences, jedrska magnetna resonanca, Kinetics, enzymatic methylation, biology.protein, thiopurine S-methyltransferase, Protein Processing, Post-Translational
Abstract

Background Methylation driven by thiopurine S-methylatransferase (TPMT) is crucial for deactivation of cytostatic and immunosuppressant thiopurines. Despite its remarkable integration into clinical practice, the endogenous function of TPMT is unknown. Methods To address the role of TPMT in methylation of selenium compounds, we established the research on saturation transfer difference (STD) and 77Se NMR spectroscopy, fluorescence measurements, as well as computational molecular docking simulations. Results Using STD NMR spectroscopy and fluorescence measurements of tryptophan residues in TPMT, we determined the binding of selenocysteine (Sec) to human recombinant TPMT. By comparing binding characteristics of Sec in the absence and in the presence of methyl donor, we confirmed S-adenosylmethionine (SAM)-induced conformational changes in TPMT. Molecular docking analysis positioned Sec into the active site of TPMT with orientation relevant for methylation reaction. Se-methylselenocysteine (MeSec), produced in the enzymatic reaction, was detected by 77Se NMR spectroscopy. A direct interaction between Sec and SAM in the active site of rTPMT and the formation of both products, MeSec and S-adenosylhomocysteine, was demonstrated using NMR spectroscopy. Conclusions The present study provides evidence on in vitro methylation of Sec by rTPMT in a SAM-dependant manner. General Significance. Our results suggest novel role of TPMT and demonstrate new insights into enzymatic modifications of the 21st amino acid. Bibliografija: str. 188-190. Abstract. ARRS ARRS ARRS

Published
2021

3. Novel motif of variable number of tandem repeats in TPMT promoter region and evolutionary association of variable number of tandem repeats with TPMT∗3 alleles

Author

Gabriele Stocco, Alenka Šmid, Giuliana Decorti, Nataša Karas Kuželički, Irena Mlinarič-Raščan, Dunja Urbančič, Urbančič, Dunja, Šmid, Alenka, Stocco, Gabriele, Decorti, Giuliana, Mlinarič-Raščan, Irena, and Karas Kuželički, Nataša

Subjects
0301 basic medicine, Heterozygote, Linkage disequilibrium, Genotype, lymphoblastoid cell lines, VNTR, Single-nucleotide polymorphism, variable number of tandem repeat, acute lymphoblastic leukemia, Biology, Polymorphism, Single Nucleotide, Linkage Disequilibrium, White People, Cell Line, 03 medical and health sciences, Thiopurine S-Methyltransferase, genetic polymorphisms, Genetic, inflammatory bowel disease, TPMT, Genetics, Humans, genetic polymorphism, linkage disequilibrium, thiopurine S-methyltransferase, TPMT activity, variable number of tandem repeats, Molecular Medicine, Pharmacology, Allele, Promoter Regions, Genetic, Gene, Alleles, Thiopurine methyltransferase, Methyltransferases, Variable number tandem repeat, Phenotype, 030104 developmental biology, Pharmacogenetics, Tandem Repeat Sequences, lymphoblastoid cell line, Pharmacogenomics, biology.protein
Abstract

Aim: SNPs in the gene for TPMT exemplify one of the most successful translations of pharmacogenomics into clinical practice. This study explains the correlation between common SNPs and variable number of tandem repeats (VNTR) in promoter of the gene. Materials & methods: We determined VNTR polymorphisms, as well as TPMT*2 and TPMT*3 SNPs and TPMT activity in Slovenian and Italian individuals and lymphoblastoid cell lines. Results: We observed a previously unreported VNTR allele, AB7C, in a TPMT*3A heterozygous individual. VNTRs with two (AB2C) and three or more (ABnC, n ≥ 3) B motifs were statistically significant in complete linkage disequilibrium (D′ = 1, r2 = 1, p

Published
2018
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