1. Proteolytically activated CRAC effectors through designed intramolecular inhibitionVid Jazbec, Roman Jerala, Mojca Benčina, 2022, original scientific article Keywords: STIM1, Orai, TEV protease, PPV protease, calcium signaling, coiled-coil peptides
Published in DiRROS: 20.07.2022; Views: 269; Downloads: 213
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3. Robust saliva-based RNA extraction-free one-step nucleic acid amplification test for mass SARS-CoV-2 monitoringEva Rajh, Tina Šket, Arne Praznik, Petra Sušjan, Alenka Šmid, Dunja Urbančič, Irena Mlinarič-Raščan, Polona Kogovšek, Tina Demšar, Mojca Milavec, Katarina Prosenc, Žiga Jensterle, Mihaela Zidarn, Viktorija Tomič, Gabriele Turel, Tatjana Lejko-Zupanc, Roman Jerala, Mojca Benčina, 2021, original scientific article 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.
Keywords: SARS-CoV-2, COVID-19, COVID-19 serological testing, real-time polymerase chain reaction, saliva, oral cavity swab, passive drool, pooling
Published in DiRROS: 09.11.2021; Views: 705; Downloads: 421
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4. Triangular in vivo self-assembling coiled-coil protein origamiSabina Božič Abram, Helena Gradišar, Jana Aupič, Adam Round, Roman Jerala, 2021, original scientific article Keywords: coiled coil, enzyme clustering, biosynthesis, resveratrol, mevalonate
Published in DiRROS: 22.03.2021; Views: 1067; Downloads: 727
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8. Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivoAjasja Ljubetič, Fabio Lapenta, Helena Gradišar, Igor Drobnak, Jana Aupič, Žiga Strmšek, Duško Lainšček, Iva Hafner Bratkovič, Andreja Majerle, Nuša Krivec, Mojca Benčina, Tomaž Pisanski, Tanja Ćirković-Veličković, Adam Round, José María Carazo, Roberto Melero, Roman Jerala, 2017, original scientific article Published in DiRROS: 17.04.2018; Views: 3398; Downloads: 2158
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9. Molecular basis of the functional differences between soluble human versus murine MD-2 : role of Val [sup] 135 in transfer of lipopolysaccharide from CD14 to MD-2Jožica Vašl, Alja Oblak, Tina Tinkara Peternelj, Javier Klett, Sonsoles Martín-Santamaría, Theresa L. Gioannini, Jerrold P. Weiss, Roman Jerala, 2016, original scientific article Keywords: MD-2, TLR-4, species specificity, innate immunology
Published in DiRROS: 10.11.2016; Views: 4447; Downloads: 975
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10. Design principles for rapid folding of knotted DNA nanostructuresVid Kočar, John S. Schreck, Slavko Čeru, Helena Gradišar, Nino Bašić, Tomaž Pisanski, Jonathan P. K. Doye, Roman Jerala, 2016, original scientific article Abstract: Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the "free-end" rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins.
Published in DiRROS: 13.04.2016; Views: 3992; Downloads: 1222
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