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Štular D, de Velde NV, Drinčić A, Kogovšek P, Filipić A, Fric K, Simončič B, Tomšič B, Chouhan RS, Bohm S, Kr. Verma S, Panda PK, Jerman I. Boosting Copper Biocidal Activity by Silver Decoration and Few-Layer Graphene in Coatings on Textile Fibers. Glob Chall 2023; 7:2300113. [PMID: 37829680 PMCID: PMC10566802 DOI: 10.1002/gch2.202300113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/26/2023] [Indexed: 10/14/2023]
Abstract
The outbreak of the Coronavirus disease 2019 (COVID-19) pandemic has highlighted the importance of developing antiviral surface coatings that are capable of repelling pathogens and neutralizing them through self-sanitizing properties. In this study, a novel coating design based on few-layer graphene (FLG) is proposed and silver-decorated micro copper flakes (CuMF) that exhibit both antibacterial and antiviral properties. The role of sacrificial anode surfaces and intrinsic graphene defects in enhancing the release of metal ions from CuMF embedded in water-based binders is investigated. In silico analysis is conducted to better understand the molecular interactions of pathogen-repelling species with bacterial or bacteriophage proteins. The results show that the optimal amount of CuMF/FLG in the coating leads to a significant reduction in bacterial growth, with reductions of 3.17 and 9.81 log for Staphylococcus aureus and Escherichia coli, respectively. The same coating also showed high antiviral efficacy, reducing bacteriophage phi6 by 5.53 log. The antiviral efficiency of the coating is find to be doubled compared to either micro copper flakes or few-layer graphene alone. This novel coating design is versatile and can be applied to various substrates, such as personal protective clothing and face masks, to provide biocidal activity against both bacterial and viral pathogens.
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Affiliation(s)
- Danaja Štular
- National Institute of ChemistryHajdrihova 19Ljubljana1001Slovenia
| | | | - Ana Drinčić
- National Institute of ChemistryHajdrihova 19Ljubljana1001Slovenia
| | - Polona Kogovšek
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Arijana Filipić
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Katja Fric
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Barbara Simončič
- Faculty of Natural Sciences and EngineeringUniversity of LjubljanaAškerčeva 12Ljubljana1000Slovenia
| | - Brigita Tomšič
- Faculty of Natural Sciences and EngineeringUniversity of LjubljanaAškerčeva 12Ljubljana1000Slovenia
| | - Raghuraj S. Chouhan
- Institute “Jožef Stefan”Department of Environmental SciencesJamova 39Ljubljana1000Slovenia
| | - Sivasambu Bohm
- Imperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Suresh Kr. Verma
- Ångströmlaboratoriet Lägerhyddsv1 Box 530Uppsala75121Sweden
- School of BiotechnologyKIIT UniversityBhubaneswar751024India
| | | | - Ivan Jerman
- National Institute of ChemistryHajdrihova 19Ljubljana1001Slovenia
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2
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Plohl O, Kokol V, Filipić A, Fric K, Kogovšek P, Fratnik ZP, Vesel A, Kurečič M, Robič J, Gradišnik L, Maver U, Zemljič LF. Screen-printing of chitosan and cationised cellulose nanofibril coatings for integration into functional face masks with potential antiviral activity. Int J Biol Macromol 2023; 236:123951. [PMID: 36898451 PMCID: PMC9995302 DOI: 10.1016/j.ijbiomac.2023.123951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Masks proved to be necessary protective measure during the COVID-19 pandemic, but they provided a physical barrier rather than inactivating viruses, increasing the risk of cross-infection. In this study, high-molecular weight chitosan and cationised cellulose nanofibrils were screen-printed individually or as a mixture onto the inner surface of the first polypropylene (PP) layer. First, biopolymers were evaluated by various physicochemical methods for their suitability for screen-printing and antiviral activity. Second, the effect of the coatings was evaluated by analysing the morphology, surface chemistry, charge of the modified PP layer, air permeability, water-vapour retention, add-on, contact angle, antiviral activity against the model virus phi6 and cytotoxicity. Finally, the functional PP layers were integrated into face masks, and resulting masks were tested for wettability, air permeability, and viral filtration efficiency (VFE). Air permeability was reduced for modified PP layers (43 % reduction for kat-CNF) and face masks (52 % reduction of kat-CNF layer). The antiviral potential of the modified PP layers against phi6 showed inhibition of 0.08 to 0.97 log (pH 7.5) and cytotoxicity assay showed cell viability above 70 %. VFE of the masks remained the same (~99.9 %), even after applying the biopolymers, confirming that these masks provided high level of protection against viruses.
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Affiliation(s)
- Olivija Plohl
- University of Maribor, Faculty of Mechanical Engineering, Smetanova ulica 17, 2000 Maribor, Slovenia.
| | - Vanja Kokol
- University of Maribor, Faculty of Mechanical Engineering, Smetanova ulica 17, 2000 Maribor, Slovenia.
| | - Arijana Filipić
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | - Katja Fric
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | - Polona Kogovšek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | - Zdenka Peršin Fratnik
- University of Maribor, Faculty of Mechanical Engineering, Smetanova ulica 17, 2000 Maribor, Slovenia.
| | - Alenka Vesel
- Jožef Stefan Institute, Department of Surface Engineering and Optoelectronics, Teslova 30, 1000 Ljubljana, Slovenia.
| | - Manja Kurečič
- University of Maribor, Faculty of Mechanical Engineering, Smetanova ulica 17, 2000 Maribor, Slovenia.
| | - Jure Robič
- Omega Air d.o.o Ljubljana, Cesta Dolomitskega odreda 10, 1000 Ljubljana, Slovenia.
| | - Lidija Gradišnik
- University of Maribor, Faculty of Medicine, Institute of Biomedical Sciences, Taborska ulica 8, 2000 Maribor, Slovenia.
| | - Uroš Maver
- University of Maribor, Faculty of Medicine, Institute of Biomedical Sciences, Taborska ulica 8, 2000 Maribor, Slovenia.
| | - Lidija Fras Zemljič
- University of Maribor, Faculty of Mechanical Engineering, Smetanova ulica 17, 2000 Maribor, Slovenia.
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3
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Filipić A, Fric K, Ravnikar M, Kogovšek P. Assessment of Different Experimental Setups to Determine Viral Filtration Efficiency of Face Masks. Int J Environ Res Public Health 2022; 19:15353. [PMID: 36430072 PMCID: PMC9690668 DOI: 10.3390/ijerph192215353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
As a result of the COVID-19 pandemic, many new materials and masks came onto the market. To determine their suitability, several standards specify which properties to test, including bacterial filtration efficiency (BFE), while none describe how to determine viral filtration efficiency (VFE), a property that is particularly important in times of pandemic. Therefore, we focused our research on evaluating the suitability and efficiency of different systems for determining VFE. Here, we evaluated the VFE of 6 mask types (e.g., a surgical mask, a respirator, material for mask production, and cloth masks) with different filtration efficiencies in four experimental setups and compared the results with BFE results. The study included 17 BFE and 22 VFE experiments with 73 and 81 mask samples tested, respectively. We have shown that the masks tested had high VFE (>99% for surgical masks and respirators, ≥98% for material, and 87-97% for cloth masks) and that all experimental setups provided highly reproducible and reliable VFE results (coefficient of variation < 6%). Therefore, the VFE tests described in this study can be integrated into existing standards for mask testing.
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4
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Sedej I, Štalekar M, Tušek Žnidarič M, Goričar K, Kojc N, Kogovšek P, Dolžan V, Arnol M, Lenassi M. Extracellular vesicle-bound DNA in urine is indicative of kidney allograft injury. J Extracell Vesicles 2022; 11:e12268. [PMID: 36149031 PMCID: PMC9503341 DOI: 10.1002/jev2.12268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/29/2022] [Accepted: 09/09/2022] [Indexed: 11/11/2022] Open
Abstract
Extracellular vesicle‐bound DNA (evDNA) is an understudied extracellular vesicle (EV) cargo, particularly in cancer‐unrelated research. Although evDNA has been detected in urine, little is known about its characteristics, localization, and biomarker potential for kidney pathologies. To address this, we enriched EVs from urine of well‐characterized kidney transplant recipients undergoing allograft biopsy, characterized their evDNA and its association to allograft injury. The SEC‐based method enriched pure EVs from urine of kidney transplant recipients, regardless of the allograft injury. Urinary evDNA represented up to 29.2 ± 8% (mean ± SD) of cell‐free DNA (cfDNA) and correlated with cfDNA in several characteristics but was less fragmented (P < 0.001). Importantly, using DNase treatment and immunogold labelling TEM, we demonstrated that evDNA was bound to the surface of urinary EVs. Normalised evDNA yield (P = 0.042) and evDNA copy number (P = 0.027) significantly differed between patients with normal histology, rejection injury and non‐rejection injury, the later groups having significantly larger uEVs (mean diameter, P = 0.045) and more DNA bound per uEV. ddDNA is detectable in uEV samples of kidney allograft recipients, but its quantity is highly variable. In a proof‐of‐principle study, several evDNA characteristics correlated with clinical and histological parameters (P = 0.040), supporting that the potential of evDNA as a biomarker for kidney allograft injury should be further investigated.
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Affiliation(s)
- Ivana Sedej
- Department of Nephrology, Division of Internal Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia.,Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Štalekar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Katja Goričar
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nika Kojc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Vita Dolžan
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Arnol
- Department of Nephrology, Division of Internal Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia.,Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Metka Lenassi
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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5
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Plohl O, Fric K, Filipić A, Kogovšek P, Tušek Žnidarič M, Zemljič LF. First Insights into the Antiviral Activity of Chitosan-Based Bioactive Polymers towards the Bacteriophage Phi6: Physicochemical Characterization, Inactivation Potential, and Inhibitory Mechanisms. Polymers (Basel) 2022; 14:polym14163357. [PMID: 36015613 PMCID: PMC9413598 DOI: 10.3390/polym14163357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The outbreak of the worrisome coronavirus disease in 2019 has caused great concern among the global public, especially regarding the need for personal protective equipment with applied antiviral agents to reduce the spread and transmission of the virus. Thus, in our research, chitosan-based bioactive polymers as potential antiviral agents were first evaluated as colloidal macromolecular solutions by elemental analysis and charge. Three different types of low and high molecular weight chitosan (LMW Ch, HMW Ch) and a LMW Ch derivative, i.e., quaternary chitosan (quart-LMW Ch), were used. To explore their antiviral activity for subsequent use in the form of coatings, the macromolecular Chs dispersions were incubated with the model virus phi6 (surrogate for SARS-CoV-2), and the success of virus inactivation was determined. Inactivation of phi6 with some chitosan-based compounds was very successful (>6 log), and the mechanisms behind this were explored. The changes in viral morphology after incubation were observed and the changes in infrared bands position were determined. In addition, dynamic and electrophoretic light scattering studies were performed to better understand the interaction between Chs and phi6. The results allowed us to better understand the antiviral mode of action of Chs agents as a function of their physicochemical properties.
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Affiliation(s)
- Olivija Plohl
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
- Correspondence: ; Tel.: +386-2-229-7715
| | - Katja Fric
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Arijana Filipić
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Lidija Fras Zemljič
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
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6
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Rajh E, Šket T, Praznik A, Sušjan P, Šmid A, Urbančič D, Mlinarič-Raščan I, Kogovšek P, Demšar T, Milavec M, Prosenc Trilar K, Jensterle Ž, Zidarn M, Tomič V, Turel G, Lejko-Zupanc T, Jerala R, Benčina M. Robust Saliva-Based RNA Extraction-Free One-Step Nucleic Acid Amplification Test for Mass SARS-CoV-2 Monitoring. Molecules 2021; 26:6617. [PMID: 34771026 PMCID: PMC8588466 DOI: 10.3390/molecules26216617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 01/19/2023] Open
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.
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Affiliation(s)
- Eva Rajh
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Tina Šket
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Petra Sušjan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Alenka Šmid
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.Š.); (D.U.); (I.M.-R.)
| | - Dunja Urbančič
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.Š.); (D.U.); (I.M.-R.)
| | - Irena Mlinarič-Raščan
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.Š.); (D.U.); (I.M.-R.)
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia; (P.K.); (T.D.); (M.M.)
| | - Tina Demšar
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia; (P.K.); (T.D.); (M.M.)
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia; (P.K.); (T.D.); (M.M.)
| | - Katarina Prosenc Trilar
- National Laboratory of Health, Environment, and Food, Laboratory for Public Health Virology, SI-1000 Ljubljana, Slovenia; (K.P.T.); (Ž.J.)
| | - Žiga Jensterle
- National Laboratory of Health, Environment, and Food, Laboratory for Public Health Virology, SI-1000 Ljubljana, Slovenia; (K.P.T.); (Ž.J.)
| | - Mihaela Zidarn
- Emergency Service, Health Centre Jesenice, SI-4270 Jesenice, Slovenia;
| | - Viktorija Tomič
- University Clinic of Respiratory and Allergic Diseases, SI-4204 Golnik, Slovenia;
| | - Gabriele Turel
- Department for Infectious Diseases, University Medical Center Ljubljana, SI-1000 Ljubljana, Slovenia; (G.T.); (T.L.-Z.)
| | - Tatjana Lejko-Zupanc
- Department for Infectious Diseases, University Medical Center Ljubljana, SI-1000 Ljubljana, Slovenia; (G.T.); (T.L.-Z.)
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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7
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Jerič Kokelj B, Štalekar M, Vencken S, Dobnik D, Kogovšek P, Stanonik M, Arnol M, Ravnikar M. Feasibility of Droplet Digital PCR Analysis of Plasma Cell-Free DNA From Kidney Transplant Patients. Front Med (Lausanne) 2021; 8:748668. [PMID: 34692738 PMCID: PMC8531215 DOI: 10.3389/fmed.2021.748668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/03/2022] Open
Abstract
Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patients' plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA.
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Affiliation(s)
- Barbara Jerič Kokelj
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Štalekar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Miha Arnol
- Department of Nephrology, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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8
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Zupančič M, Kogovšek P, Šter T, Remec Rekar Š, Cerasino L, Baebler Š, Krivograd Klemenčič A, Eleršek T. Potentially Toxic Planktic and Benthic Cyanobacteria in Slovenian Freshwater Bodies: Detection by Quantitative PCR. Toxins (Basel) 2021; 13:toxins13020133. [PMID: 33670338 PMCID: PMC7917684 DOI: 10.3390/toxins13020133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Due to increased frequency of cyanobacterial blooms and emerging evidence of cyanotoxicity in biofilm, reliable methods for early cyanotoxin threat detection are of major importance for protection of human, animal and environmental health. To complement the current methods of risk assessment, this study aimed to evaluate selected qPCR assays for detection of potentially toxic cyanobacteria in environmental samples. In the course of one year, 25 plankton and 23 biofilm samples were collected from 15 water bodies in Slovenia. Three different analyses were performed and compared to each other; qPCR targeting mcyE, cyrJ and sxtA genes involved in cyanotoxin production, LC-MS/MS quantifying microcystin, cylindrospermopsin and saxitoxin concentration, and microscopic analyses identifying potentially toxic cyanobacterial taxa. qPCR analyses detected potentially toxic Microcystis in 10 lake plankton samples, and potentially toxic Planktothrix cells in 12 lake plankton and one lake biofilm sample. A positive correlation was observed between numbers of mcyE gene copies and microcystin concentrations. Potential cylindrospermopsin- and saxitoxin-producers were detected in three and seven lake biofilm samples, respectively. The study demonstrated a potential for cyanotoxin production that was left undetected by traditional methods in both plankton and biofilm samples. Thus, the qPCR method could be useful in regular monitoring of water bodies to improve risk assessment and enable timely measures.
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Affiliation(s)
- Maša Zupančič
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia;
- Jozef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
- Correspondence:
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia; (P.K.); (Š.B.)
| | - Tadeja Šter
- Slovenian Environment Agency, 1000 Ljubljana, Slovenia; (T.Š.); (Š.R.R.); (A.K.K.)
| | - Špela Remec Rekar
- Slovenian Environment Agency, 1000 Ljubljana, Slovenia; (T.Š.); (Š.R.R.); (A.K.K.)
| | - Leonardo Cerasino
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia; (P.K.); (Š.B.)
| | | | - Tina Eleršek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia;
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9
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Dobnik D, Kogovšek P, Jakomin T, Košir N, Tušek Žnidarič M, Leskovec M, Kaminsky SM, Mostrom J, Lee H, Ravnikar M. Accurate Quantification and Characterization of Adeno-Associated Viral Vectors. Front Microbiol 2019; 10:1570. [PMID: 31379763 PMCID: PMC6650692 DOI: 10.3389/fmicb.2019.01570] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
One of the main challenges in the gene therapy viral vector development is to establish an optimized process for its large scale production. This requires optimization for upstream and downstream processes as well as methods that enable the step-by step analytical characterization of the virus, the results of which inform the iterative refinement of production for yield, purity and potency. The biggest problem here is a plethora of viral vector formulations, many of which interfere with analytical techniques. We took adeno-associated virus (AAV) as an example and showed benefits of combined use of molecular methods and transmission electron microscopy (TEM) for viral vectors' characterization and quantification. Results of the analyses showed that droplet digital PCR (ddPCR) performs better than quantitative real-time PCR (qPCR), in terms of robustness and assay variance, and this was especially relevant for partially purified (in-process) samples. Moreover, we demonstrate the importance of sample preparation prior to PCR analysis. We evaluated viral structure, presence of aggregates and impurities with TEM analysis and found that these impacted the differences in viral titers observed by qPCR and ddPCR and could be altered by sample preparation. These results serve as a guide for the establishment of the analytical methods required to provide measures of identity and purity for AAV viral vectors.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tjaša Jakomin
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Nejc Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Stephen M Kaminsky
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Janet Mostrom
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Hyunmi Lee
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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10
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Kogovšek P, Ambrožič-Avguštin J, Dovč A, Dreo T, Hristov H, Krapež U, Ravnikar M, Slavec B, Lotrič M, Žel J, Zorman Rojs O. Loop-mediated isothermal amplification: rapid molecular detection of virulence genes associated with avian pathogenic Escherichia coli in poultry. Poult Sci 2019; 98:1500-1510. [PMID: 30476321 PMCID: PMC6377436 DOI: 10.3382/ps/pey516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/18/2018] [Indexed: 11/20/2022] Open
Abstract
Infections with pathogenic Escherichia coli can lead to different animal- and human-associated diseases. E. coli infections are common in intensive poultry farming, and important economic losses can be expected during infections with avian pathogenic E. coli (APEC) strains followed by colibacillosis. Loop-mediated isothermal amplification (LAMP) assays were developed for rapid detection of 3 APEC-associated virulence genes: sitA, traT, and ompT. All 3 LAMP assays are shown to be specific, repeatable, and reproducible. High sensitivities of the assays are shown, where as few as 1,000 bacterial cells/mL can be detected in different matrices. On-site applicability of this LAMP method is demonstrated through testing of different sample types, from animal swabs and tissues, and from environmental samples collected from 6 commercial poultry farms. All 3 virulence genes were detected at high rates (above 85%) in samples from layer and broiler chickens with clinical signs and, interestingly, high prevalence of those genes was detected also in samples collected from clinically healthy broiler flock (above 75%) while lower prevalence was observed in remaining 3 clinically healthy chicken flocks (less than 75%). Importantly, these virulence genes were detected in almost all of the air samples from 11 randomly selected poultry houses, indicating air as an important route of E. coli spread. Three LAMP assays that target APEC-associated virulence genes are shown to be sensitive and robust and are therefore applicable for rapid on-site testing of various sample types, from animal swabs to air. This on-site LAMP testing protocol offers rapid diagnostics, with results obtained in <35 min, and it can be applied to other important microorganisms to allow the required prompt measures to be taken.
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Affiliation(s)
| | | | - Alenka Dovč
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tanja Dreo
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Hristo Hristov
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Uroš Krapež
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, 1000 Ljubljana, Slovenia.,Wine Research Centre, University of Nova Gorica, 5000 Nova Gorica, Slovenia
| | - Brigita Slavec
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
| | | | - Jana Žel
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Olga Zorman Rojs
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
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11
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Miklavič Š, Kogovšek P, Hodnik V, Korošec J, Kladnik A, Anderluh G, Gutierrez-Aguirre I, Maček P, Butala M. The Pseudomonas aeruginosa RhlR-controlled aegerolysin RahU is a low-affinity rhamnolipid-binding protein. FEMS Microbiol Lett 2015; 362:fnv069. [PMID: 25926530 DOI: 10.1093/femsle/fnv069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2015] [Indexed: 01/18/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa uses quorum-sensing systems to regulate collective behaviour in response to the environment, by linking the expression of particular genes to population density. The quorum-sensing transcription factors LasR and RhlR and their cognate N-acyl-homoserine lactone (HSL) signals N-3-oxo-dodecanoyl-L-HSL (3OC12-HSL) and N-butanoyl-L-HSL (C4-HSL) control the expression of several hundred genes, which include those involved in virulence and biofilm formation. Here, we have focused on regulation of the expression of the putative virulence factor gene, rahU. We show that the intact las-rhl box immediately upstream of the -35 promoter element is needed for rahU expression in P. aeruginosa. Using β-galactosidase assays and quantification of the mRNA levels for rahU, lasR and rhlR, we provide evidence that for rahU promoter activity, 3OC12-HSL-LasR is not sufficient, and instead C4-HSL-RhlR is the trigger. Furthermore, surface plasmon resonance analysis revealed that RahU binds the biosurfactant rhamnolipids. Thus, this is the first report of a bacterial molecule that interacts with RahU.
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Affiliation(s)
- Špela Miklavič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Vesna Hodnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Korošec
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Kladnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Ion Gutierrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Peter Maček
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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12
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Kogovšek P, Hodgetts J, Hall J, Prezelj N, Nikolić P, Mehle N, Lenarčič R, Rotter A, Dickinson M, Boonham N, Dermastia M, Ravnikar M. LAMP assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine. Plant Pathol 2015; 64:286-296. [PMID: 26146413 PMCID: PMC4480326 DOI: 10.1111/ppa.12266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/21/2014] [Indexed: 05/23/2023]
Abstract
In Europe the most devastating phytoplasma associated with grapevine yellows (GY) diseases is a quarantine pest, flavescence dorée (FDp), from the 16SrV taxonomic group. The on-site detection of FDp with an affordable device would contribute to faster and more efficient decisions on the control measures for FDp. Therefore, a real-time isothermal LAMP assay for detection of FDp was validated according to the EPPO standards and MIQE guidelines. The LAMP assay was shown to be specific and extremely sensitive, because it detected FDp in all leaf samples that were determined to be FDp infected using quantitative real-time PCR. The whole procedure of sample preparation and testing was designed and optimized for on-site detection and can be completed in one hour. The homogenization procedure of the grapevine samples (leaf vein, flower or berry) was optimized to allow direct testing of crude homogenates with the LAMP assay, without the need for DNA extraction, and was shown to be extremely sensitive.
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Affiliation(s)
- P Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
- Department of Biology, Biotechnical Faculty, University of LjubljanaVečna pot 111, 1000, Ljubljana, SIovenia
| | - J Hodgetts
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - J Hall
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - N Prezelj
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - P Nikolić
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - N Mehle
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - R Lenarčič
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - A Rotter
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - M Dickinson
- School of Biosciences, University of NottinghamSutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - N Boonham
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - M Dermastia
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - M Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
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13
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Petek M, Rotter A, Kogovšek P, Baebler S, Mithöfer A, Gruden K. Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack. Mol Ecol 2014; 23:5378-91. [PMID: 25251011 PMCID: PMC4237146 DOI: 10.1111/mec.12932] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 09/16/2014] [Accepted: 09/17/2014] [Indexed: 01/07/2023]
Abstract
In the field, plants are challenged by more than one biotic stressor at the same time. In this study, the molecular interactions between potato (Solanum tuberosum L.), Colorado potato beetle (Leptinotarsa decemlineata Say; CPB) and Potato virus Y(NTN) (PVY(NTN) ) were investigated through analyses of gene expression in the potato leaves and the gut of the CPB larvae, and of the release of potato volatile compounds. CPB larval growth was enhanced when reared on secondary PVY(NTN) -infected plants, which was linked to decreased accumulation of transcripts associated with the antinutritional properties of potato. In PVY(NTN) -infected plants, ethylene signalling pathway induction and induction of auxin response transcription factors were attenuated, while no differences were observed in jasmonic acid (JA) signalling pathway. Similarly to rearing on virus-infected plants, CPB larvae gained more weight when reared on plants silenced in JA receptor gene (coi1). Although herbivore-induced defence mechanism is regulated predominantly by JA, response in coi1-silenced plants only partially corresponded to the one observed in PVY(NTN) -infected plants, confirming the role of other plant hormones in modulating this response. The release of β-barbatene and benzyl alcohol was different in healthy and PVY(NTN) -infected plants before CPB larvae infestation, implicating the importance of PVY(NTN) infection in plant communication with its environment. This was reflected in gene expression profiles of neighbouring plants showing different degree of defence response. This study thus contributes to our understanding of plant responses in agro-ecosystems.
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Affiliation(s)
- Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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14
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Rupar M, Kogovšek P, Pompe-Novak M, Gutiérrez-Aguirre I, Delaunay A, Jacquot E, Ravnikar M. Assessment of SNaPshot and single step RT-qPCR methods for discriminating Potato virus Y (PVY) subgroups. J Virol Methods 2013; 189:93-100. [PMID: 23396125 DOI: 10.1016/j.jviromet.2013.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 01/23/2013] [Accepted: 01/28/2013] [Indexed: 11/30/2022]
Abstract
Potato virus Y (PVY) is the most important virus infecting potato (Solanum tuberosum), causing potato tuber necrotic ringspot disease (PTNRD), with a great impact on seed potato production. Numerous PVY strain groups with different pathogenicity and economical impact are distributed worldwide. Tools for accurate and reliable detection and discrimination of PVY strain groups are therefore essential for successful disease management. Two state of the art characterization tools based on detecting molecular markers - RT-qPCR (Kogovsek et al., 2008) and SNaPshot (Rolland et al., 2008) - were assessed for their ability to assign PVY accurately to the correct group. The results were validated by bioassay, ELISA and in silico sequence analysis. The spectrum of PVY strain groups distinguished by SNaPshot is broader than that by RT-qPCR. However, the latter was more reliable in discriminating the PVY(NTN) group members, known for their ability to induce PTNRD on selected potato cultivars. The difference in discrimination precision was due to different molecular markers being targeted by RT-qPCR and SNaPshot. Both tools use genotypic markers for detecting PVY(NTN) strain groups. Future development, however, should be focused on identifying the genomic determinants of the tuber necrosis property. Until then, the RT-qPCR and SNaPshot methods remain the most powerful diagnostic tools for detecting the PVY subgroup isolates found in Europe.
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Affiliation(s)
- Matevž Rupar
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
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15
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Dobnik D, Baebler Š, Kogovšek P, Pompe-Novak M, Štebih D, Panter G, Janež N, Morisset D, Žel J, Gruden K. β-1,3-glucanase class III promotes spread of PVY NTN and improves in planta protein production. Plant Biotechnol Rep 2013; 7:547-555. [PMID: 24273610 PMCID: PMC3824212 DOI: 10.1007/s11816-013-0300-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/11/2013] [Indexed: 05/18/2023]
Abstract
Glucanases are enzymes regulating the size exclusion limit and permeability of plasmodesmata and play a role in biotic stress. In plant genomes, they are encoded as relatively large gene families divided into four classes. Most studies of plant virus interactions have focused on glucanases from classes I and II. In our study, we have evaluated the role of the β-1,3-glucanase class III (Glu-III) gene in the potato-potato virus YNTN (PVYNTN) interaction and implemented the findings to plant biotechnology application. Potato cultivars Désirée and Santé, which are tolerant and extremely resistant to PVYNTN, respectively, were stably transformed with Agrobacterium tumefaciens harbouring constructs for Glu-III overexpression. Localization of Glu-III protein in patches within the cell wall was determined by tagging the Glu-III protein with green fluorescent protein. Transgenic and non-transgenic plants were challenged with PVYNTN and its multiplication and spreading was followed. Differences in viral spread were observed between transgenic lines overexpressing Glu-III and non-transgenic lines, with stronger and faster viral spread in transgenic Désirée, and some multiplication in transgenic Santé. In addition, the ability of Glu-III to improve in planta protein production after agroinfiltration was tested. The results have shown that Glu-III overexpression enables faster spreading of vectors between cells and better protein production, which could be beneficial in improving in planta protein production system using viral vectors.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Maruša Pompe-Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Dejan Štebih
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Gabriela Panter
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Nikolaja Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Velika pot 22, 5250 Solkan, Slovenia
| | - Dany Morisset
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Velika pot 22, 5250 Solkan, Slovenia
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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16
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Baebler Š, Stare K, Kovač M, Blejec A, Prezelj N, Stare T, Kogovšek P, Pompe-Novak M, Rosahl S, Ravnikar M, Gruden K. Dynamics of responses in compatible potato-Potato virus Y interaction are modulated by salicylic acid. PLoS One 2011; 6:e29009. [PMID: 22194976 PMCID: PMC3237580 DOI: 10.1371/journal.pone.0029009] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 11/18/2011] [Indexed: 12/21/2022] Open
Abstract
To investigate the dynamics of the potato – Potato virus Y (PVY) compatible interaction in relation to salicylic acid - controlled pathways we performed experiments using non-transgenic potato cv. Désirée, transgenic NahG-Désirée, cv. Igor and PVYNTN, the most aggressive strain of PVY. The importance of salicylic acid in viral multiplication and symptom development was confirmed by pronounced symptom development in NahG-Désirée, depleted in salicylic acid, and reversion of the effect after spraying with 2,6-dichloroisonicotinic acid (a salicylic acid - analogue). We have employed quantitative PCR for monitoring virus multiplication, as well as plant responses through expression of selected marker genes of photosynthetic activity, carbohydrate metabolism and the defence response. Viral multiplication was the slowest in inoculated potato of cv. Désirée, the only asymptomatic genotype in the study. The intensity of defence-related gene expression was much stronger in both sensitive genotypes (NahG-Désirée and cv. Igor) at the site of inoculation than in asymptomatic plants (cv. Désirée). Photosynthesis and carbohydrate metabolism gene expression differed between the symptomatic and asymptomatic phenotypes. The differential gene expression pattern of the two sensitive genotypes indicates that the outcome of the interaction does not rely simply on one regulatory component, but similar phenotypical features can result from distinct responses at the molecular level.
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Affiliation(s)
- Špela Baebler
- Department for Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
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17
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Kogovšek P, Kladnik A, Mlakar J, Znidarič MT, Dermastia M, Ravnikar M, Pompe-Novak M. Distribution of Potato virus Y in potato plant organs, tissues, and cells. Phytopathology 2011; 101:1292-300. [PMID: 21692643 DOI: 10.1094/phyto-01-11-0020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The distribution of Potato virus Y (PVY) in the systemically infected potato (Solanum tuberosum) plants of the highly susceptible cultivar Igor was investigated. Virus presence and accumulation was analyzed in different plant organs and tissues using real-time polymerase chain reaction and transmission electron microscopy (TEM) negative staining methods. To get a complete insight into the location of viral RNA within the tissue, in situ hybridization was developed and optimized for the detection of PVY RNA at the cellular level. PVY was shown to accumulate in all studied leaf and stem tissues, in shoot tips, roots, and tubers; however, the level of virus accumulation was specific for each organ or tissue. The highest amounts of viral RNA and viral particles were found in symptomatic leaves and stem. By observing cell ultrastructure with TEM, viral cytoplasmic inclusion bodies were localized in close vicinity to the epidermis and in trichomes. Our results show that viral RNA, viral particles, and cytoplasmic inclusion bodies colocalize within the same type of cells or in close vicinity.
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Affiliation(s)
- P Kogovšek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia.
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18
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Kogovšek P, Gow L, Pompe-Novak M, Gruden K, Foster G, Boonham N, Ravnikar M. Single-step RT real-time PCR for sensitive detection and discrimination of Potato virus Y isolates. J Virol Methods 2008; 149:1-11. [DOI: 10.1016/j.jviromet.2008.01.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/16/2008] [Accepted: 01/21/2008] [Indexed: 10/22/2022]
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