756 results on '"Kurg A"'
Search Results
2. Microfluidic production, stability and loading of synthetic giant unilamellar vesicles
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Mart Ernits, Olavi Reinsalu, Naresh Yandrapalli, Sergei Kopanchuk, Ehsan Moradpur-Tari, Immanuel Sanka, Ott Scheler, Ago Rinken, Reet Kurg, Andreas Kyritsakis, Veikko Linko, and Veronika Zadin
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Medicine ,Science - Abstract
Abstract In advanced drug delivery, versatile liposomal formulations are commonly employed for safer and more accurate therapies. Here we report a method that allows a straightforward production of synthetic monodisperse (~ 100 μm) giant unilamellar vesicles (GUVs) using a microfluidic system. The stability analysis based on the microscopy imaging showed that at ambient conditions the produced GUVs had a half-life of 61 ± 2 h. However, it was observed that ~ 90% of the calcein dye that was loaded into GUVs was transported into a surrounding medium in 24 h, thus indicating that the GUVs may release these small dye molecules without distinguishable membrane disruption. We further demonstrated the feasibility of our method by loading GUVs with larger and very different cargo objects; small soluble fluorescent proteins and larger magnetic microparticles in a suspension. Compared to previously reported microfluidics-based production techniques, the obtained results indicate that our simplified method could be equally harnessed in creating GUVs with less cost, effort and time, which could further benefit studying closed membrane systems.
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- 2024
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3. Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss
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Essers, Rick, Lebedev, Igor N., Kurg, Ants, Fonova, Elizaveta A., Stevens, Servi J. C., Koeck, Rebekka M., von Rango, Ulrike, Brandts, Lloyd, Deligiannis, Spyridon Panagiotis, Nikitina, Tatyana V., Sazhenova, Elena A., Tolmacheva, Ekaterina N., Kashevarova, Anna A., Fedotov, Dmitry A., Demeneva, Viktoria V., Zhigalina, Daria I., Drozdov, Gleb V., Al-Nasiry, Salwan, Macville, Merryn V. E., van den Wijngaard, Arthur, Dreesen, Jos, Paulussen, Aimee, Hoischen, Alexander, Brunner, Han G., Salumets, Andres, and Zamani Esteki, Masoud
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- 2023
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4. Boosted production of antibodies that neutralized different SARS-CoV-2 variants in a COVID-19 convalescent following messenger RNA vaccination - a case study
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Erlend Ravlo, Aleksandr Ianevski, Eirin Starheim, Wei Wang, Ping Ji, Hilde Lysvand, Teemu Smura, Gaily Kivi, Maia-Liisa Voolaid, Kati Plaan, Mart Ustav, Mart Ustav, Jr., Eva Zusinaite, Tanel Tenson, Reet Kurg, Valentyn Oksenych, Kirsti Walstad, Svein Arne Nordbø, Mari Kaarbø, Karin Ernits, Magnar Bjørås, Denis E. Kainov, and Mona Høysæter Fenstad
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SARS-CoV-2 ,COVID-19 ,mRNA vaccination ,Immune response ,Neutralizing antibody ,Infectious and parasitic diseases ,RC109-216 - Abstract
Vaccinated convalescents do not develop severe COVID-19 after infection with new SARS-CoV-2 variants. We questioned how messenger RNA (mRNA) vaccination of convalescents provides protection from emerging virus variants. From the cohort of 71 convalescent plasma donors, we identified a patient who developed immune response to infection with SARS-CoV-2 variant of 20A clade and who subsequently received mRNA vaccine encoding spike (S) protein of strain of 19A clade. We showed that vaccination increased the production of immune cells and anti-S antibodies in the serum. Serum antibodies neutralized not only 19A and 20A, but also 20B, 20H, 21J, and 21K virus variants. One of the serum antibodies (100F8) completely neutralized 20A, 21J, and partially 21K strains. 100F8 was structurally similar to published Ab188 antibody, which recognized non-conserved epitope on the S protein. We proposed that 100F8 and other serum antibodies of the patient which recognized non- and conserved epitopes of the S protein, could have additive or synergistic effects to neutralize various virus variants. Thus, mRNA vaccination could be beneficial for convalescents because it boosts production of neutralizing antibodies with broad-spectrum activity.
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- 2023
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5. The combination of pleconaril, rupintrivir, and remdesivir efficiently inhibits enterovirus infections in vitro, delaying the development of drug-resistant virus variants
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Ianevski, Aleksandr, Frøysa, Irene Trøen, Lysvand, Hilde, Calitz, Carlemi, Smura, Teemu, Schjelderup Nilsen, Hans-Johnny, Høyer, Erling, Afset, Jan Egil, Sridhar, Adithya, Wolthers, Katja C., Zusinaite, Eva, Tenson, Tanel, Kurg, Reet, Oksenych, Valentyn, Galabov, Angel S., Stoyanova, Adelina, Bjørås, Magnar, and Kainov, Denis E.
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- 2024
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6. The methyltransferase N6AMT1 participates in the cell cycle by regulating cyclin E levels.
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Margit Mutso, Baiba Brūmele, Evgeniia Serova, Fred Väärtnõu, Mihkel Suija, and Reet Kurg
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Medicine ,Science - Abstract
The methyltransferase N6AMT1 has been associated with the progression of different pathological conditions, such as tumours and neurological malfunctions, but the underlying mechanism is not fully understood. Analysis of N6AMT1-depleted cells revealed that N6AMT1 is involved in the cell cycle and cell proliferation. In N6AMT1-depleted cells, the cell doubling time was increased, and cell progression out of mitosis and the G0/G1 and S phases was disrupted. It was discovered that in N6AMT1-depleted cells, the transcription of cyclin E was downregulated, which indicates that N6AMT1 is involved in the regulation of cyclin E transcription. Understanding the functions and importance of N6AMT1 in cell proliferation and cell cycle regulation is essential for developing treatments and strategies to control diseases that are associated with N6AMT1.
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- 2024
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7. Barley and wheat beta-glucan content influenced by weather, fertilization, and genotype
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Banafsheh Khaleghdoust, Keyvan Esmaeilzadeh-Salestani, Mailiis Korge, Maarika Alaru, Kaidi Möll, Rando Värnik, Reine Koppel, Ülle Tamm, Max Kurg, Illimar Altosaar, and Evelin Loit
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beta-glucan ,nitrogen ,dietary fiber ,cropping system ,organic ,conventional ,Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
IntroductionBeta-glucan is one of the most important dietary fibers in cereal grains, having a great impact on human health and food quality. Wheat and barley are strategic crops and their fibers contribute toward their nutraceutical impact. However, the health of the environment is also important to ensure sustainable crop production. Hence the European decision makers have agreed to move toward organic cropping and to reduce the use of mineral fertilizers. Environment and agricultural management have a vast impact on the content of β-glucan in cereal grains. To exploit the valuable properties of β-glucan, the knowledge of factors increasing the amount of this component is crucial. We hypothesized that annual weather conditions, nitrogen fertilization, and cropping system affect the β-glucan amount in wheat and barley.MethodsFor this purpose, spring barley and winter wheat flour samples from an 8-year-long period (2014-2021) were characterized. The experiment included conventional and organic cropping systems with different nitrogen rates between 0 and 150 kg ha−1. In addition, the variation of β-glucan content in different varieties was analyzed.Results and discussionThe results showed that the content of β-glucan in barley and wheat grains was affected mainly by weather conditions not by fertilization. The latter finding means that the regulation of crop nutrition is not going to impact dietary fiber content in our everyday food. Lower temperatures during tillering and higher 1,000 kernel weight and test weight showed a positive correlation with β-glucan content in barley grains, while precipitation during the grain filling period had a negative correlation. Our findings suggest that β-glucan can be obtained from low-input and organic systems as efficiently as from fertilized treatments. However, there is a need for adaptation strategies in industry, as β-glucan content can vary from year to year.
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- 2024
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8. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes
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Toome Kadri, Parkel Sven, Palta Priit, Glynn Barry, Kaplinski Lauris, Scheler Ott, Maher Majella, Barry Thomas, Remm Maido, and Kurg Ants
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Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.
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- 2011
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9. Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides
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Palta Priit, Parkel Sven, Scheler Ott, Kaplinski Lauris, Toome Kadri, Kurg Ants, and Remm Maido
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Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background The hybridization of synthetic Streptococcus pneumoniae tmRNA on a detection microarray is slow at 34°C resulting in low signal intensities. Results We demonstrate that adding specific DNA helper oligonucleotides (chaperones) to the hybridization buffer increases the signal strength at a given temperature and thus makes the specific detection of Streptococcus pneumoniae tmRNA more sensitive. No loss of specificity was observed at low temperatures compared to hybridization at 46°C. The effect of the chaperones can be explained by disruption of the strong secondary and tertiary structure of the target RNA by the selective hybridization of helper molecules. The amplification of the hybridization signal strength by chaperones is not necessarily local; we observed increased signal intensities in both local and distant regions of the target molecule. Conclusions The sensitivity of the detection of tmRNA at low temperature can be increased by chaperone oligonucleotides. Due to the complexity of RNA secondary and tertiary structures the effect of any individual chaperone is currently not predictable.
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- 2010
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10. Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications
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Kaplinski Lauris, Toome Kadri, Palta Priit, Parkel Sven, Glynn Barry, Scheler Ott, Remm Maido, Maher Majella, and Kurg Ants
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Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background Here we present a novel promising microbial diagnostic method that combines the sensitivity of Nucleic Acid Sequence Based Amplification (NASBA) with the high information content of microarray technology for the detection of bacterial tmRNA molecules. The NASBA protocol was modified to include aminoallyl-UTP (aaUTP) molecules that were incorporated into nascent RNA during the NASBA reaction. Post-amplification labeling with fluorescent dye was carried out subsequently and tmRNA hybridization signal intensities were measured using microarray technology. Significant optimization of the labeled NASBA protocol was required to maintain the required sensitivity of the reactions. Results Two different aaUTP salts were evaluated and optimum final concentrations were identified for both. The final 2 mM concentration of aaUTP Li-salt in NASBA reaction resulted in highest microarray signals overall, being twice as high as the strongest signals with 1 mM aaUTP Na-salt. Conclusion We have successfully demonstrated efficient combination of NASBA amplification technology with microarray based hybridization detection. The method is applicative for many different areas of microbial diagnostics including environmental monitoring, bio threat detection, industrial process monitoring and clinical microbiology.
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- 2009
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11. Primer Extension From Two-Dimensional Oligonucleotides Grids for Dna Sequence Analysis
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Metspalu, A., primary, Saulep, H., additional, Kurg, A., additional, Tõnisson, N., additional, and Shumaker, J.M., additional
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- 2023
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12. Cross-Reactivity of N6AMT1 Antibodies with Aurora Kinase A: An Example of Antibody-Specific Non-Specificity
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Baiba Brūmele, Evgeniia Serova, Aleksandra Lupp, Mihkel Suija, Margit Mutso, and Reet Kurg
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methyltransferase ,N6AMT1 ,AURKA ,antibodies ,cross-reactivity ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Primary antibodies are one of the main tools used in molecular biology research. However, the often-occurring cross-reactivity of primary antibodies complicates accurate data analysis. Our results show that three commercial polyclonal antibodies raised against N-6 adenine-specific DNA methyltransferase 1 (N6AMT1) strongly cross-react with endogenous and recombinant mitosis-associated protein Aurora kinase A (AURKA). The cross-reactivity was verified through immunofluorescence, immunoblot, and immunoprecipitation assays combined with mass spectrometry. N6AMT1 and AURKA are evolutionarily conserved proteins that are vital for cellular processes. Both proteins share the motif ENNPEE, which is unique to only these two proteins. We suggest that N6AMT1 antibodies recognise this motif in N6AMT1 and AURKA proteins and exhibit an example of “specific” non-specificity. This serves as an example of the importance of controls and critical data interpretation in molecular biology research.
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- 2024
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13. How the Intrinsically Disordered N-Terminus of Cancer/Testis Antigen MAGEA10 Is Responsible for Its Expression, Nuclear Localisation and Aberrant Migration
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Anneli Samel, Fred Väärtnõu, Lisbeth Verk, Kristiina Kurg, Margit Mutso, and Reet Kurg
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cancer/testis antigens ,MAGEA10 ,intrinsically disordered proteins ,nuclear localization ,protein stability ,Microbiology ,QR1-502 - Abstract
Melanoma-associated antigen A (MAGEA) subfamily proteins are normally expressed in testis and/or placenta. However, aberrant expression is detected in the tumour cells of multiple types of human cancer. MAGEA expression is mainly observed in cancers that have acquired malignant phenotypes, invasiveness and metastasis, and the expression of MAGEA family proteins has been linked to poor prognosis in cancer patients. All MAGE proteins share the common MAGE homology domain (MHD) which encompasses up to 70% of the protein; however, the areas flanking the MHD region vary between family members and are poorly conserved. To investigate the molecular basis of MAGEA10 expression and anomalous mobility in gel, deletion and point-mutation, analyses of the MAGEA10 protein were performed. Our data show that the intrinsically disordered N-terminal domain and, specifically, the first seven amino acids containing a unique linear motif, PRAPKR, are responsible for its expression, aberrant migration in SDS-PAGE and nuclear localisation. The aberrant migration in gel and nuclear localisation are not related to each other. Hiding the N-terminus with an epitope tag strongly affected its mobility in gel and expression in cells. Our results suggest that the intrinsically disordered domains flanking the MHD determine the unique properties of individual MAGEA proteins.
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- 2023
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14. How the Intrinsically Disordered N-Terminus of Cancer/Testis Antigen MAGEA10 Is Responsible for Its Expression, Nuclear Localisation and Aberrant Migration
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Samel, Anneli, primary, Väärtnõu, Fred, additional, Verk, Lisbeth, additional, Kurg, Kristiina, additional, Mutso, Margit, additional, and Kurg, Reet, additional
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- 2023
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15. Cross-Reactivity of N6AMT1 Antibodies with Aurora Kinase A: An Example of Antibody-Specific Non-Specificity.
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Brūmele, Baiba, Serova, Evgeniia, Lupp, Aleksandra, Suija, Mihkel, Mutso, Margit, and Kurg, Reet
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AURORA kinases ,MOLECULAR biology ,RECOMBINANT proteins ,CROSS reactions (Immunology) ,IMMUNOGLOBULINS ,METHYLGUANINE - Abstract
Primary antibodies are one of the main tools used in molecular biology research. However, the often-occurring cross-reactivity of primary antibodies complicates accurate data analysis. Our results show that three commercial polyclonal antibodies raised against N-6 adenine-specific DNA methyltransferase 1 (N6AMT1) strongly cross-react with endogenous and recombinant mitosis-associated protein Aurora kinase A (AURKA). The cross-reactivity was verified through immunofluorescence, immunoblot, and immunoprecipitation assays combined with mass spectrometry. N6AMT1 and AURKA are evolutionarily conserved proteins that are vital for cellular processes. Both proteins share the motif ENNPEE, which is unique to only these two proteins. We suggest that N6AMT1 antibodies recognise this motif in N6AMT1 and AURKA proteins and exhibit an example of "specific" non-specificity. This serves as an example of the importance of controls and critical data interpretation in molecular biology research. [ABSTRACT FROM AUTHOR]
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- 2024
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16. Barley and wheat beta-glucan content influenced by weather, fertilization, and genotype
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Khaleghdoust, Banafsheh, primary, Esmaeilzadeh-Salestani, Keyvan, additional, Korge, Mailiis, additional, Alaru, Maarika, additional, Möll, Kaidi, additional, Värnik, Rando, additional, Koppel, Reine, additional, Tamm, Ülle, additional, Kurg, Max, additional, Altosaar, Illimar, additional, and Loit, Evelin, additional
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- 2024
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17. In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages
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Zamani Esteki, Masoud, Viltrop, Triin, Tšuiko, Olga, Tiirats, Airi, Koel, Mariann, Nõukas, Margit, Žilina, Olga, Teearu, Katre, Marjonen, Heidi, Kahila, Hanna, Meekels, Jeroen, Söderström-Anttila, Viveca, Suikkari, Anne-Maria, Tiitinen, Aila, Mägi, Reedik, Kõks, Sulev, Kaminen-Ahola, Nina, Kurg, Ants, Voet, Thierry, Vermeesch, Joris Robert, and Salumets, Andres
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- 2019
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18. The methyltransferase N6AMT1 participates in the cell cycle by regulating cyclin E levels.
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Mutso, Margit, Brūmele, Baiba, Serova, Evgeniia, Väärtnõu, Fred, Suija, Mihkel, and Kurg, Reet
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CELL cycle ,CELL cycle regulation ,CYCLINS ,METHYLTRANSFERASES ,CELL proliferation ,CELL analysis - Abstract
The methyltransferase N6AMT1 has been associated with the progression of different pathological conditions, such as tumours and neurological malfunctions, but the underlying mechanism is not fully understood. Analysis of N6AMT1-depleted cells revealed that N6AMT1 is involved in the cell cycle and cell proliferation. In N6AMT1-depleted cells, the cell doubling time was increased, and cell progression out of mitosis and the G0/G1 and S phases was disrupted. It was discovered that in N6AMT1-depleted cells, the transcription of cyclin E was downregulated, which indicates that N6AMT1 is involved in the regulation of cyclin E transcription. Understanding the functions and importance of N6AMT1 in cell proliferation and cell cycle regulation is essential for developing treatments and strategies to control diseases that are associated with N6AMT1. [ABSTRACT FROM AUTHOR]
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- 2024
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19. Boosted production of antibodies which neutralized different SARS-CoV-2 variants in a COVID-19 convalescent following mRNA vaccination – a case study
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Ravlo, Erlend, primary, Ianevski, Aleksandr, additional, Starheim, Eirin, additional, Wang, Wei, additional, Ji, Ping, additional, Lysvand, Hilde, additional, Smura, Teemu, additional, Kivi, Gaily, additional, Voolaid, Maia-Liisa, additional, Plaan, Kati, additional, Ustav, Mart, additional, Zusinaite, Eva, additional, Tenson, Tanel, additional, Kurg, Reet, additional, Oksenych, Valentyn, additional, Walstad, Kirsti, additional, Nordbø, Svein Arne, additional, Kaarbø, Mari, additional, Ernits, Karin, additional, Bjørås, Magnar, additional, Kainov, Denis E., additional, and Høysæter Fenstad, Mona, additional
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- 2023
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20. Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor
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Baiba Brūmele, Margit Mutso, Lilian Telanne, Kadri Õunap, Karīna Spunde, Aare Abroi, and Reet Kurg
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methyltransferase ,TRMT112 ,RNA methylation ,ribosome biogenesis ,protein stabilisation ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Methylation is an essential epigenetic modification mainly catalysed by S-Adenosyl methionine-dependent methyltransferases (MTases). Several MTases require a cofactor for their metabolic stability and enzymatic activity. TRMT112 is a small evolutionary conserved protein that acts as a co-factor and activator for different MTases involved in rRNA, tRNA and protein methylation. Using a SILAC screen, we pulled down seven methyltransferases—N6AMT1, WBSCR22, METTL5, ALKBH8, THUMPD2, THUMPD3 and TRMT11—as interaction partners of TRMT112. We showed that TRMT112 stabilises all seven MTases in cells. TRMT112 and MTases exhibit a strong mutual feedback loop when expressed together in cells. TRMT112 interacts with its partners in a similar way; however, single amino acid mutations on the surface of TRMT112 reveal several differences as well. In summary, mammalian TRMT112 can be considered as a central “hub” protein that regulates the activity of at least seven methyltransferases.
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- 2021
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21. Evaluating the Arrayed Primer Extension Resequencing Assay of TP53 Tumor Suppressor Gene
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Tõnisson, Neeme, Zernant, Jana, Kurg, Ants, Pavel, Hendrik, Slavin, Georg, Roomere, Hanno, Meiel, Aune, Hainaut, Pierre, and Metspalu, Andres
- Published
- 2002
22. Target prediction and validation of microRNAs expressed from FSHR and aromatase genes in human ovarian granulosa cells
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Rooda, Ilmatar, Hensen, Kati, Kaselt, Birgitta, Kasvandik, Sergo, Pook, Martin, Kurg, Ants, Salumets, Andres, and Velthut-Meikas, Agne
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- 2020
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23. Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis)
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Jekaterina Erenpreisa, Jekabs Krigerts, Kristine Salmina, Bogdan I. Gerashchenko, Talivaldis Freivalds, Reet Kurg, Ruth Winter, Matthias Krufczik, Pawel Zayakin, Michael Hausmann, and Alessandro Giuliani
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chromatin organization ,heterochromatin ,networks ,positional information ,scale-free oscillations ,nucleolar boundary ,Cytology ,QH573-671 - Abstract
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.
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- 2021
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24. MAGEA4 Coated Extracellular Vesicles Are Stable and Can Be Assembled In Vitro
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Olavi Reinsalu, Anneli Samel, Elen Niemeister, and Reet Kurg
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extracellular vesicles ,cancer-testis antigen ,MAGEA4 ,recombinant protein ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Extracellular vesicles (EVs) are valued candidates for the development of new tools for medical applications. Vesicles carrying melanoma-associated antigen A (MAGEA) proteins, a subfamily of cancer-testis antigens, are particularly promising tools in the fight against cancer. Here, we have studied the biophysical and chemical properties of MAGEA4-EVs and show that they are stable under common storage conditions such as keeping at +4 °C and −80 °C for at least 3 weeks after purification. The MAGEA4-EVs can be freeze-thawed two times without losing MAGEA4 in detectable quantities. The attachment of MAGEA4 to the surface of EVs cannot be disrupted by high salt concentrations or chelators, but the vesicles are sensitive to high pH. The MAGEA4 protein can bind to the surface of EVs in vitro, using robust passive incubation. In addition, EVs can be loaded with recombinant proteins fused to the MAGEA4 open reading frame within the cells and also in vitro. The high stability of MAGEA4-EVs ensures their potential for the development of EV-based anti-cancer applications.
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- 2021
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25. Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP.
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Tõnis Org, Kati Hensen, Rita Kreevan, Elina Mark, Olav Sarv, Reidar Andreson, Ülle Jaakma, Andres Salumets, and Ants Kurg
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Medicine ,Science - Abstract
Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited. Here we describe a novel method called Restriction Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables global histone modification profiling from as few as 100 cells. The method is simple, cost-effective and takes a single day to complete. We demonstrate the sensitivity of the method by deriving the first genome-wide maps of histone H3K4me3 and H3K27me3 modifications of inner cell mass and trophectoderm of bovine blastocyst stage embryos.
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- 2019
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26. Architecture and the Environment
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Sophie Hochhäusl, Torsten Lange, Ross Exo Adams, Daniel A. Barber, Aleksandr Bierig, Kenny Cupers, Isabelle Doucet, Jennifer Ferng, Sabine von Fischer, Kim Förster, Maroš Krivý, Andres Kurg, Ayala Levin, Ginger Nolan, and Alla Vronskaya
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Architecture ,NA1-9428 - Abstract
These Field Notes, on the topic of Architecture and the Environment, elucidate how problems raised in the environmental humanities have informed architectural history, and in turn, what architectural history has to contribute to this emerging field. The short essays explore specific ‘positions’ in the overarching debate, identifying a radical return to critical theory and the embrace of the fundamentally transdisciplinary nature of environmental humanities and architectural history. While the positions advocate for a serious investigation of architects’ texts and ideas on environmental issues, the collection also champions a broader engagement with Anthropocene questions and proposes to adopt the environment as an intellectual perspective from which to look upon the world.
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- 2018
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27. Primer Extension From Two-Dimensional Oligonucleotides Grids for Dna Sequence Analysis
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A. Metspalu, H. Saulep, A. Kurg, N. Tõnisson, and J.M. Shumaker
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- 2023
28. A dual colour FISH method for routine validation of sexed Bos taurus semen
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Reinsalu, Olavi, Scheler, Ott, Mikelsaar, Ruth, Mikelsaar, Aavo-Valdur, Hallap, Triin, Jaakma, Ülle, Padrik, Peeter, Kavak, Ants, Salumets, Andres, and Kurg, Ants
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- 2019
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29. Tallinn in Technicolour
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Kurg, Andres
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- 2015
30. Identification and Tracking of Antiviral Drug Combinations
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Aleksandr Ianevski, Rouan Yao, Svetlana Biza, Eva Zusinaite, Andres Mannik, Gaily Kivi, Anu Planken, Kristiina Kurg, Eva-Maria Tombak, Mart Ustav, Nastassia Shtaida, Evgeny Kulesskiy, Eunji Jo, Jaewon Yang, Hilde Lysvand, Kirsti Løseth, Valentyn Oksenych, Per Arne Aas, Tanel Tenson, Astra Vitkauskienė, Marc P. Windisch, Mona Høysæter Fenstad, Svein Arne Nordbø, Magnar Bjørås, and Denis E. Kainov
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antivirals ,antiviral drug combinations ,broad-spectrum antivirals ,virus ,Microbiology ,QR1-502 - Abstract
Combination therapies have become a standard for the treatment for HIV and hepatitis C virus (HCV) infections. They are advantageous over monotherapies due to better efficacy, reduced toxicity, as well as the ability to prevent the development of resistant viral strains and to treat viral co-infections. Here, we identify new synergistic combinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), echovirus 1 (EV1), hepatitis C virus (HCV) and human immunodeficiency virus 1 (HIV-1) in vitro. We observed synergistic activity of nelfinavir with convalescent serum and with purified neutralizing antibody 23G7 against SARS-CoV-2 in human lung epithelial Calu-3 cells. We also demonstrated synergistic activity of nelfinavir with EIDD-2801 or remdesivir in Calu-3 cells. In addition, we showed synergistic activity of vemurafenib with emetine, homoharringtonine, anisomycin, or cycloheximide against EV1 infection in human lung epithelial A549 cells. We also found that combinations of sofosbuvir with brequinar or niclosamide are synergistic against HCV infection in hepatocyte-derived Huh-7.5 cells, and that combinations of monensin with lamivudine or tenofovir are synergistic against HIV-1 infection in human cervical TZM-bl cells. These results indicate that synergy is achieved when a virus-directed antiviral is combined with another virus- or host-directed agent. Finally, we present an online resource that summarizes novel and known antiviral drug combinations and their developmental status.
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- 2020
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31. Seven Views on the Meaning of ‘Europe’
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Christian Freigang, Andres Kurg, Ana Tostões, Carmen Popescu, Rob Dettingmeijer, Nancy Stieber, and Christine Mengin
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Architecture ,NA1-9428 - Abstract
The first part of these field notes consists of three perspectives from Germany, Estonia, and Portugal on the meaning of ‘Europe’ for the historiography of architecture. The second part contains four reflections on the history and role of the EAHN in opening new and inclusive venues of inquiry vis-à-vis the fragile concept of ‘Europe’.
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- 2018
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32. Proteomic and Biochemical Analysis of Extracellular Vesicles Isolated from Blood Serum of Patients with Melanoma
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Kristiina Kurg, Anu Planken, and Reet Kurg
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Filtration and Separation ,Analytical Chemistry ,melanoma ,extracellular vesicles ,purification ,ultracentrifugation ,PEG precipitation - Abstract
Background: Malignant melanoma is the most serious type of skin cancer with the highest mortality rate. Extracellular vesicles (EVs) have potential as new tumor markers that could be used as diagnostic and prognostic markers for early detection of melanoma. Methods: EVs were purified from the blood serum of melanoma patients using two methods—ultracentrifugation and PEG precipitation—and analyzed by mass spectrometry and immunoblot. Results: We identified a total of 585 unique proteins; 334 proteins were detected in PEG-precipitated samples and 515 in UC-purified EVs. EVs purified from patients varied in their size and concentration in different individuals. EVs obtained from stage II and III patients were, on average, smaller and more abundant than others. Detailed analysis of three potential biomarkers—SERPINA3, LGALS3BP, and gelsolin—revealed that the expression of SERPINA3 and LGALS3BP was higher in melanoma patients than healthy controls, while gelsolin exhibited higher expression in healthy controls. Conclusion: We suggest that all three proteins might have potential to be used as biomarkers, but a number of issues, such as purification of EVs, standardization, and validation of methods suitable for everyday clinical settings, still need to be addressed.
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- 2022
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33. Proteomic and Biochemical Analysis of Extracellular Vesicles Isolated from Blood Serum of Patients with Melanoma
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Kurg, Kristiina, primary, Planken, Anu, additional, and Kurg, Reet, additional
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- 2022
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34. Genome stability of bovine in vivo-conceived cleavage-stage embryos is higher compared to in vitro-produced embryos
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Tšuiko, Olga, Catteeuw, Maaike, Zamani Esteki, Masoud, Destouni, Aspasia, Bogado Pascottini, Osvaldo, Besenfelder, Urban, Havlicek, Vitezslav, Smits, Katrien, Kurg, Ants, Salumets, Andres, D’Hooghe, Thomas, Voet, Thierry, Van Soom, Ann, and Robert Vermeesch, Joris
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- 2017
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35. Courtyards, Corners, Streetfronts: Re-Imagining Mass Housing Areas in Tallinn
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Kurg, Andres, primary
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- 2016
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36. Oxidative Properties of Blood-Derived Extracellular Vesicles in 15 Patients After Myocardial Infarction
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Žėkas, Vytautas, primary, Kurg, Reet, additional, Kurg, Kristiina, additional, Bironaitė, Daiva, additional, Radzevičius, Mantas, additional, Karčiauskaitė, Dovilė, additional, Matuzevičienė, Rėda, additional, and Kučinskienė, Zita Aušrelė, additional
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- 2022
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37. The Common Partner of Several Methyltransferases TRMT112 Regulates the Expression of N6AMT1 Isoforms in Mammalian Cells
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Lilian Leetsi, Kadri Õunap, Aare Abroi, and Reet Kurg
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methyltransferase ,TRMT112 ,alternative splicing ,N6AMT1 ,protein stability ,Microbiology ,QR1-502 - Abstract
Methylation is a widespread modification occurring in DNA, RNA and proteins. The N6AMT1 (HEMK2) protein has DNA N6-methyladenine as well as the protein glutamine and histone lysine methyltransferase activities. The human genome encodes two different isoforms of N6AMT1, the major isoform and the alternatively spliced isoform, where the substrate binding motif is missing. Several RNA methyltransferases involved in ribosome biogenesis, tRNA methylation and translation interact with the common partner, the TRMT112 protein. In this study, we show that TRMT112 regulates the expression of N6AMT1 isoforms in mammalian cells. Both isoforms are equally expressed on mRNA level, but only isoform 1 is detected on the protein level in human cells. We show that the alternatively spliced isoform is not able to interact with TRMT112 and when translated, is rapidly degraded from the cells. This suggests that TRMT112 is involved in cellular quality control ensuring that N6AMT1 isoform with missing substrate binding domain is eliminated from the cells. The down-regulation of TRMT112 does not affect the N6AMT1 protein levels in cells, suggesting that the two proteins of TRMT112 network, WBSCR22 and N6AMT1, are differently regulated by their common cofactor.
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- 2019
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38. Label-free, multiplexed detection of bacterial tmRNA using silicon photonic microring resonators
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Scheler, Ott, Kindt, Jared T., Qavi, Abraham J., Kaplinski, Lauris, Glynn, Barry, Barry, Thomas, Kurg, Ants, and Bailey, Ryan C.
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- 2012
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39. Lapsehoidjate tööstressi ja läbipõlemist mõjutavad tegurid Tartu linna näitel
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Kurg, Liana and Merisalu, Eda
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vaimne tervis ,emotsionaalne kurnatus ,lapsehoidja ,magistritööd ,ergonoomiline sekkumine - Abstract
Magistritöö Ergonoomika õppekaval Lapsehoidja (child care worker) on erialase väljaõppe saanud lastega vahetult töötav lasteasutuses või kodukeskkonnas töötav isik. Ootused pädevale lapsehoidjale on kõrged ning töö vastutusrikas. Eesmärk: analüüsida lapsehoidjate töö eripärast tulenevaid psühhosotsiaalseid tegureid ja läbipõlemise indikaatoreid, hinnata nende näitajate mõju töötajate tervisele ning koostada lapsehoidja vaimset tervist toetava ergonoomikalise sekkumiskava näidisprogramm. Metoodika: uuritavateks olid Tartu linna lastehoidudes min 1-a tööstaažiga lapsehoidja kutsetunnistust omavad töötajad (n=105), katsegrupis oli 42 lapsehoidjat. Uuringus kasutati rahvusvaheliselt valideeritud ankeetküsimustikke: psühhosotsiaalsete ohutegurite küsimustik COPSOQ II (Copenhagen Psychososcial Questionnaire); läbipõlemisküsimustik MBI (Maslach Burnout Inventory), kus mõõdiku skaalad hindasid probleemi esinemissagedust (s) ja häirivustugevust (t) 3 läbipõlemise indikaatori suhtes: emotsionaalne kurnatus (EKs, EKt), depersonalisatsioon (DPs, DPt) ja professionaalne efektiivsus (PEs, PEt). Ergonoomikalise sekkumiskava väljatöötamiseks viidi läbi seminaripäev. Tulemused: küsimustikule vastas 105 lapsehoidjat, kõik olid naissoost, peamiselt 30– 39 a, keskmine tööstaaž 5,1 a (±2,2 aastat). Enamus (95,2%) töötas täistööajaga päevases vahetuses. Ületunnitööd tegi 10,4% vastanutest. Kõrgemate keskmiste skooridega hinnati töökohal arenguvõimalusi, võimalust õppida uusi asju (x̄203,0;±49,5), tööle pühendumist (x̄208,0;±56,6), rahulolu tööga (x̄207,8;±53,3). Madalamad skoorid anti faktorgruppidele kvantitatiivsed nõudmised, mõju töö üle, unehäired (x̄66,7;±20,7), läbipõlemine (x̄47,1;±20). Konflikte ja ebameeldivat käitumist töökohal esines vähe (x̄3,7;±9,3). Lapsehoidjate töös esineb keskmisel määral läbipõlemise ilminguid, enim märgiti ära emotsionaalset kurnatust nii EKs kui EKt nätajates ning seda eeskätt nooremas vanusegrupis. Oma professionaalse efektiivsuse (PEs, PEt) ja depersonalisatsiooni ilmingud (DPs, DPt) hinnati valdavalt keskmiseks. Kõrgeim skoor anti EKs 72,8% ja PEt 70,5%. Kui võrrelda esinemissageduse ja häirivisutugevuse näitajaid, siis EKs hinnatakse kõrgemalt (x̄=26,5; α=0,78) kui EKt (x̄=22,8; α=0,78) (p=0,0001). Järeldused: Lapsehoidjate töös esineb psühhosotsiaalseid ohutegureid, mis on seotud liigse töökoormuse, ebavõrdse tööde jaotumise, rollikonfliktide, kõrgete emotsionaalsete nõudmiste, usaldamatuse ning otsese ülemuse poolse tunnustuse vähesusega. Oma tööd tähtsustakse, töökeskkonnatingimusi peetakse heaks, kõrgelt hinnatakse kolleegide vahelist meeskonnatööd, töö- ja pereelu konflikti, kiusamist ja vägivaldset käitumist esineb vähe. Hinnang enda tervislikule üldseisundile on hea, kuid esineb stressi, ärevust, unehäireid ja kurnatust. Lapsehoidjad, kes hindavad oma tervislikku seisundit pigem heaks, on rohkem tööle pühendunud, peavad paremaks oma arenguvõimalusi ja kõrgemaks juhtimise kvaliteeti ning kolleegide ja ülemuse poolset toetust. Kõrge EK lapsehoidjad on oluliselt rohkem mõjutatud kiirest töötempost, tähtsustavad suuremal määral oma tööd, hindavad oluliselt madalamaks otsese ülemuse poolset tunnustust ning neil esineb rohkem pere-ja tööelu konflikti, nad on vähem tööle pühendunud ja tajuvad tugevamalt rollikonflikti ning madalamat kolleegide poolset toetust. Sekkumiskava näidisprogramm keskendub töökoormuse võrdsele jaotamisele, suhtlemise ja meeskonnatöö edendamisele; teadlikkuse ja pädevuse tõstmisele. Eriti pööratakse koolitustel tähelepanu lapsehoidjate tööstressi ning läbipõlemise ennetamisele ja vaimse tervise toetamisele läbi ergonoomikalise sekkumisprogrammi, kus olulisel kohal on tervisedenduslikud tegevused. A child care worker is a professional with special training and knowledge to work with kids in a child care institutions or in home environment. Expectations about child care workers professional qualifications are high and there are great responsibility for a child's welfare. The aim of the research was to analyze the specifics of the work of child care workers as well as work related stress factors and burnout indicators and assess the impact of these indicators on the health of employees and develop a sample of ergonomic intervention program to support the mental health of child care workers. Material and method. The child care workers with professional certificate at least one year's work experience (n=105) in municipal and private child daycare institutions in Tartu constituted the study group. There were 42 child care workers in the seminar group. Internationally validated questionnaires COPSOQ II (Copenhagen Psychososcial Questionnaire) and the MBI (Maslach Burnout Inventory) burnout questionnaire were used in this research. The frequency (s) and severity (t) scales for burnout indicators were used – emotional exhaustion (EKs, EKt), depersonalization (DPs, DPt) and professional effectiveness (PEs, PEt). A seminar day was held to develop the ergonomic intervention plan. Results. 105 child care workers responded to the questionnaire, all of them female, mainly 30–39 years, with an average length of service 5,1 (± 2,2) years. The majority (95,2%) worked full-time on a daily basis and 10,4% of the respondents worked overtime. Higher average scores were used to assess development opportunities in the workplace, the opportunity to learn new things (x̄=203,0 ±49,5), work commitment (x̄=208,0± 56,6), job satisfaction (x̄=207,8±53,3). Lower scores were given to the factor groups for quantitative demands, effects on work, sleeping problems (x̄=66,7±20,7), burnout (x̄=47,1±20,0). There are few conflicts and unpleasant behavior in the workplace (x̄=3,7± 9,3). There were moderate signs of burnout, emotional exhaustion the most often noted in both EK and EK indicators, especially in the younger age group. Low professional effectiveness (PEs, PEt) and depersonalization (DPs, DPt) were predominantly moderate. The highest proportion of respondents assessed EK as moderate was 72,8% and PE 70,5%. While comparing the frequency (s) and disturbance (t) of the problems, the EK frequency is rated higher (x̄ = 26,5; α = 0,78) than the disturbance (x̄= 22,8; α = 0,78) (p = 0,0001). Conclusion: There are psychosocial risk factors in the work of child care workers which are related to excessive workload, unequal distribution of work, role conflicts, higher emotional demands, mistrust and lack of recognition by the immediate superior. Child care workers considerate their work very important, working conditions were good, teamwork between colleagues was highly valued. There were some conflict between work and family life, and rare bullying and violent behavior cases in their work. The child care workers assessed their general health as good, but also stress, anxiety, sleep problems and exhaustion were mentioned. The babysitters, whose health was better, were more committed to work. They had better opportunities for development and higher quality of management, and greater support from colleagues and superior. Child care workers with high emotional exhaustion were significantly more affected by greater work load, assesssed higher importance to their work, valued recognition from their immediate superior, had more work-family conflicts and work life, were less committed to work and had a stronger perception of role conflict and lower support of coworkers. A sample of ergonomic intervention program to support the mental health of child care workers focuses on equality of workload, communication and teamwork promotion, raising awareness of mental health and professional competence. Particular attention will be paid to the prevention of stress and burnout and promotion of mental health through the ergonomic intervention program through health promotion activities in it
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- 2022
40. Beetaglükaani sisaldus talinisu terades sõltuvalt lämmastiku normist, ilmastikust ning sordist
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Kurg, Max, Loit, Evelin, Korge, Mailiis, and Khaleghdoust, Banafsheh
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sort ,lämmastik ,bakalaureusetööd ,nisu ,ilmastik ,beetaglükaan - Abstract
Bakalaureusetöö Põllumajandussaaduste tootmise ja turustamise õppekaval Eesti põllumajanduse oluline eesmärk on suurendada tarneahelas loodavat lisandväärtust. Käesoleva bakalaureusetöö eesmärgiks oli uurida talinisu seemnete β-glükaani sisaldust sõltuvalt kasutatud lämmastiku normist, aasta ilmastikust ja kasvatatava nisu sordist ning analüüsida seoseid β-glükaani, tuhande tera massi ja saagikuse vahel. Töös analüüsiti talinisu terasid, mis olid koristatud aastatel 2020 ja 2021 seitsme väetusvariandiga (lämmastiku norm 0–150 kg ha-1 ) põldkatselt Tartus ning nelja sordiga (Fredis, Skagen, Toras, Creator) tootmispõllult Järvamaal. Lämmastiku norm ei mõjutanud β-glükaani kontsentratsiooni ning oli kahe aasta vältel stabiilne. Suurem kasvuaegne sademete hulk juunis ja juulis vähendas β-glükaani sisaldust tootmiskatses. Varajase sordi β-glükaani sisaldusele mõjus kuum ja kuiv ilm positiivselt, kuid hilisematel sortidel oli mõju vastupidine. Beetaglükaani sisaldus sõltus nisu sordist. Tootmispõllu katses leiti dispersioonanalüüsi põhjal, et β-glükaani sisalduse mõjust moodustab sort lausa 56%. Seosed β-glükaani, tuhande tera massi ja terasaagikuse vahel olid usutavad tootmispõllu katses, kus testiti nelja erinevat talinisu sorti. Tulemused on olulised teraviljade väärindamise kontekstis. Edaspidised uurimised näitavad, kas saadud tulemused kehtivad ka rohkemate aastate andmete põhjal. The aim of Estonian agriculture is to add value to its raw products. The aim of this thesis was to investigate the β-glucan content of winter wheat grains depending on nitrogen rate, the weather conditions of the year and the variety, and to analyse the relationships between β-glucan, thousand kernel weight and grain yield. Winter wheat seeds were harvested from the field trial with seven nitrogen treatments (nitrogen rate 0–150 kg ha-1 ) in Tartu and from the production field with four varieties (Fredis, Skagen, Toras, Creator) in Järvamaa in 2020 and 2021. It was found that β-glucan concentrations was stable over the two years and nitrogen rate did not affect it. Higher precipitation in June and July reduced β-glucan concentrations in the production field. The β-glucan content of the early variety was positively influenced by hot and dry weather, while late varieties had the opposite effect. The β-glucan content depended on the wheat variety. In a field trial, dispersion analysis showed that the variety accounts for 56% of the effect of β-glucan content. The relationships between β-glucan, thousand kernel weight and grain yield were statistically different in a field trial with four different winter wheat varieties. Further studies are needed to confirm the results under multi-year weather conditions.
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- 2022
41. Viroloogia. II osa. Üldine ja molekulaarne viroloogia
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Abroi, Aare, Avi, Radko, Kurg, Reet, Merits, Andres, Sarmiento, Cecilia, Sõmera, Merike, Žusinaite, Eva, and Truve, Erkki
- Published
- 2022
42. Creating basis for introducing non‐invasive prenatal testing in the Estonian public health setting
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Konstantin Ridnõi, Andres Salumets, Kadri Rekker, Tiia Reimand, Priit Paluoja, Neeme Tõnisson, Eva-Liina Ustav, Lauris Kaplinski, Martin Sauk, Priit Palta, Joris Vermeesch, Hindrek Teder, Olga Žilina, Ants Kurg, and Kaarel Krjutškov
- Subjects
0303 health sciences ,medicine.medical_specialty ,030219 obstetrics & reproductive medicine ,Massive parallel sequencing ,Obstetrics ,business.industry ,Ultrasound scan ,Non invasive ,Obstetrics and Gynecology ,Aneuploidy ,medicine.disease ,DNA extraction ,3. Good health ,03 medical and health sciences ,0302 clinical medicine ,Cell-free fetal DNA ,medicine ,Fetal Examination ,Trisomy ,business ,Genetics (clinical) ,030304 developmental biology - Abstract
OBJECTIVE The study aimed to validate a whole-genome sequencing-based NIPT laboratory method and our recently developed NIPTmer aneuploidy detection software with the potential to integrate the pipeline into prenatal clinical care in Estonia. METHOD In total, 424 maternal blood samples were included. Analysis pipeline involved cell-free DNA extraction, library preparation and massively parallel sequencing on Illumina platform. Aneuploidies were determined with NIPTmer software, which is based on counting pre-defined per-chromosome sets of unique k-mers from sequencing raw data. SeqFF was implemented to estimate cell-free fetal DNA (cffDNA) fraction. RESULTS NIPTmer identified correctly all samples of non-mosaic trisomy 21 (T21, 15/15), T18 (9/9), T13 (4/4) and monosomy X (4/4) cases, with the 100% sensitivity. However, one mosaic T18 remained undetected. Six false-positive (FP) results were observed (FP rate of 1.5%, 6/398), including three for T18 (specificity 99.3%) and three for T13 (specificity 99.3%). The level of cffDNA of
- Published
- 2019
43. In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages
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Mariann Koel, Masoud Zamani Esteki, Heidi Marjonen, Sulev Kõks, Katre Teearu, Joris Vermeesch, Ants Kurg, Jeroen Meekels, Olga Žilina, Anne-Maria Suikkari, Andres Salumets, Airi Tiirats, Thierry Voet, Reedik Mägi, Margit Nõukas, Nina Kaminen-Ahola, Aila Tiitinen, Hanna Kahila, Viveca Söderström-Anttila, Triin Viltrop, Olga Tšuiko, RS: GROW - R4 - Reproductive and Perinatal Medicine, and MUMC+: DA KG Lab Centraal Lab (9)
- Subjects
0301 basic medicine ,Male ,DNA Copy Number Variations ,Genotype ,medicine.medical_treatment ,Placenta ,Aneuploidy ,Embryonic Development ,Fertilization in Vitro ,MOSAICISM ,Biology ,Polymorphism, Single Nucleotide ,General Biochemistry, Genetics and Molecular Biology ,Andrology ,CHROMOSOME INSTABILITY ,03 medical and health sciences ,HIDDEN-MARKOV MODEL ,0302 clinical medicine ,Fetus ,BLASTOCYSTS ,Pregnancy ,Chromosome instability ,Chromosomal Instability ,medicine ,Humans ,Cell Lineage ,Blastocyst ,COMMON ,In vitro fertilisation ,ANEUPLOIDY ,ABNORMALITIES ,Embryogenesis ,Infant, Newborn ,Embryo ,General Medicine ,medicine.disease ,Embryo, Mammalian ,female genital diseases and pregnancy complications ,CONSTITUTION ,GENOME ,030104 developmental biology ,medicine.anatomical_structure ,HUMAN-EMBRYOS ,030220 oncology & carcinogenesis ,embryonic structures ,Female - Abstract
Although chromosomal instability (CIN) is a common phenomenon in cleavage-stage embryogenesis following in vitro fertilization (IVF)(1-3), its rate in naturally conceived human embryos is unknown. CIN leads to mosaic embryos that contain a combination of genetically normal and abnormal cells, and is significantly higher in in vitro-produced preimplantation embryos as compared to in vivo-conceived preimplantation embryos(4). Even though embryos with CIN-derived complex aneuploidies may arrest between the cleavage and blastocyst stages of embryogenesis(5,6), a high number of embryos containing abnormal cells can pass this strong selection barrier(7,8). However, neither the prevalence nor extent of CIN during prenatal development and at birth, following IVF treatment, is well understood. Here we profiled the genomic landscape of fetal and placental tissues postpartum from both IVF and naturally conceived children, to investigate the prevalence and persistence of large genetic aberrations that probably arose from IVF-related CIN. We demonstrate that CIN is not preserved at later stages of prenatal development, and that de novo numerical aberrations or large structural DNA imbalances occur at similar rates in IVF and naturally conceived live-born neonates. Our findings affirm that human IVF treatment has no detrimental effect on the chromosomal constitution of fetal and placental lineages.
- Published
- 2019
44. A parallel SNP array study of genomic aberrations associated with mental retardation in patients and general population in Estonia
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Männik, Katrin, Parkel, Sven, Palta, Priit, Žilina, Olga, Puusepp, Helen, Esko, Tõnu, Mägi, Reedik, Nõukas, Margit, Veidenberg, Andres, Nelis, Mari, Metspalu, Andres, Remm, Maido, Õunap, Katrin, and Kurg, Ants
- Published
- 2011
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45. Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor
- Author
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Brūmele, Baiba, primary, Mutso, Margit, additional, Telanne, Lilian, additional, Õunap, Kadri, additional, Spunde, Karīna, additional, Abroi, Aare, additional, and Kurg, Reet, additional
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- 2021
- Full Text
- View/download PDF
46. P–381 Deciphering the genetic cause of recurrent and sporadic pregnancy loss
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Ants Kurg, Han G. Brunner, G Acharya, T. V. Nikitina, Merryn V. E. Macville, Andres Salumets, R Essers, M Zaman. Esteki, S P Deligiannis, E. A. Sazhenova, Elizaveta A. Fonova, Servi J. C. Stevens, Salwan Al-Nasiry, I. N. Lebedev, and E. N. Tolmacheva
- Subjects
Pregnancy ,Reproductive Medicine ,business.industry ,Rehabilitation ,Obstetrics and Gynecology ,Physiology ,Medicine ,business ,medicine.disease - Abstract
Study question To investigate the prevalence and effect of (mosaic) de novo genomic aberrations in recurrent pregnancy loss (RPL) and sporadic abortion (SA). Summary answer Prevalence of maternal uniparental disomies (UPDs) was high in both cohorts. While chromosomal UPDs were found in both cohorts, genome wide UPDs were RPL specific. What is known already Spontaneous abortion occurs in 10–15% of clinically recognized pregnancies and recurrent pregnancy loss in 1–3%. SA and RPL are associated with reduced quality of life. Multiple factors contribute to SA and RPL, such as uterine malformations and parental/fetal chromosomal abnormalities. However, in ∼60% of SA and RPL the cause remains unknown. UPD is defined as the presence of two homologues chromosomes originating from a single parent. This phenomenon can lead to imprinting disorders that are characterised by clinical features affecting growth, development and metabolism in liveborn offspring. However, it could also be responsible for pregnancy loss. Study design, size, duration We recruited 32 families with pregnancy loss (n = 16 RPL cohort, n = 16 SA cohort) with no known genetic predispositions and normal karyotyping results in both parents and the fetus. Average maternal age was 28.68 years (SD = 5.43), paternal age 30.3 years (SD = 5.53), and the gestational age at pregnancy loss was 8.65 weeks (SD = 2.47). The average number of miscarriages in the RPL group was 3.57 (SD = 0.84). We profiled the genomic landscape of both cohorts using SNP typing. Participants/materials, setting, methods We isolated DNA from blood of both parents and the placental tissues from the miscarried products of conception. The placenta tissues were sampled from two distinct extraembryonic and embryonic germ layers, the extraembryonic mesoderm and the chorionic villi cytotrophoblast. Subsequently, we performed SNP-genotyping using Illumina’s Global-Screening Array–24 v2.0 BeadChips and applied haplarithmisis to delineate allelic architecture of fetal tissues of both cohorts. This allowed us to detect large de novo copy-number and -neutral (>10kb) changes. Main results and the role of chance In this pilot study, we have analyzed 132 DNA samples (n = 32 families), of which 16 families were in the RPL cohort and 16 in the SA cohort. Within the RPL cohort, we found: one family with mosaic genome wide hexaploidy both in the extraembryonic mesoderm and chorionic villi, one family with a non-mosaic genome wide hetero UPD of the chorionic villi tissue, one family with a mosaic UPD of chromosome 14 in both tissues and tetraploidy exclusively in the chorionic villi, one family with a mosaic UPD of chromosome 16 in both tissues, one family with a mosaic UPD of chromosome 6 in both tissues, and another family with a mosaic UPD of chromosome 5 in the extraembryonic mesoderm. Within the SA group, one family showed a UPD of chromosome 7 and another family showed a segmental UPD of chromosome 5 in both tissues. Strikingly, all the UPDs found in this study were maternal in origin. Limitations, reasons for caution The main limitation of this study is the resolution of detecting copy-neutral and copy-number variations, which is an inherent limiting factor of SNP-array technology. In addition, in the sample in which we observed non-mosaic genome wide UPD, maternal contamination is likely that can be investigated by other technologies. Wider implications of the findings: Multiple genome wide UPDs are found in the RPL group but none in the SA group, indicating an association between genome wide mosaic UPD and RPL. These findings could lead to a better understanding of causative factors for SA and RPL and the need for a SNP-based non-invasive prenatal testing. Trial registration number Not applicable
- Published
- 2021
47. MAGEA4 Coated Extracellular Vesicles Are Stable and Can Be Assembled In Vitro
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Anneli Samel, Elen Niemeister, Reet Kurg, and Olavi Reinsalu
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Octoxynol ,QH301-705.5 ,Drug Storage ,Green Fluorescent Proteins ,Extracellular vesicles ,Catalysis ,Article ,law.invention ,Inorganic Chemistry ,Mice ,Antigen ,law ,Antigens, Neoplasm ,Freezing ,Animals ,Physical and Theoretical Chemistry ,Biology (General) ,Molecular Biology ,QD1-999 ,Spectroscopy ,Chemistry ,Vesicle ,Organic Chemistry ,General Medicine ,Hydrogen-Ion Concentration ,In vitro ,Recombinant Proteins ,Computer Science Applications ,Neoplasm Proteins ,Open reading frame ,Recombinant DNA ,Biophysics ,Salts ,extracellular vesicles ,cancer-testis antigen ,recombinant protein ,MAGEA4 - Abstract
Extracellular vesicles (EVs) are valued candidates for the development of new tools for medical applications. Vesicles carrying melanoma-associated antigen A (MAGEA) proteins, a subfamily of cancer-testis antigens, are particularly promising tools in the fight against cancer. Here, we have studied the biophysical and chemical properties of MAGEA4-EVs and show that they are stable under common storage conditions such as keeping at +4 °C and −80 °C for at least 3 weeks after purification. The MAGEA4-EVs can be freeze-thawed two times without losing MAGEA4 in detectable quantities. The attachment of MAGEA4 to the surface of EVs cannot be disrupted by high salt concentrations or chelators, but the vesicles are sensitive to high pH. The MAGEA4 protein can bind to the surface of EVs in vitro, using robust passive incubation. In addition, EVs can be loaded with recombinant proteins fused to the MAGEA4 open reading frame within the cells and also in vitro. The high stability of MAGEA4-EVs ensures their potential for the development of EV-based anti-cancer applications.
- Published
- 2021
48. Boosted production of antibodies that neutralized different SARS-CoV-2 variants in a COVID-19 convalescent following messenger RNA vaccination - a case study
- Author
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Ravlo, Erlend, Ianevski, Aleksandr, Starheim, Eirin, Wang, Wei, Ji, Ping, Lysvand, Hilde, Smura, Teemu, Kivi, Gaily, Voolaid, Maia-Liisa, Plaan, Kati, Ustav, Mart, Ustav, Mart, Jr., Zusinaite, Eva, Tenson, Tanel, Kurg, Reet, Oksenych, Valentyn, Walstad, Kirsti, Nordbø, Svein Arne, Kaarbø, Mari, Ernits, Karin, Bjørås, Magnar, Kainov, Denis E., and Fenstad, Mona Høysæter
- Published
- 2023
- Full Text
- View/download PDF
49. Free communication: from Soviet future cities to kitchen conversations
- Author
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Andres Kurg
- Subjects
Visual Arts and Performing Arts ,Urban planning ,Political economy ,Political science ,media_common.quotation_subject ,Architecture ,Marxist philosophy ,Ideology ,Relation (history of concept) ,Soviet union ,Communism ,Communication theory ,media_common - Abstract
This article looks at discussions of communist urban planning in relation to both the Marxist theory of ideology and communication theory in the 1960s in the Soviet Union, and the ways in which the...
- Published
- 2019
50. Introduction: urban planning and architecture of late socialism
- Author
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Daria Bocharnikova and Andres Kurg
- Subjects
Visual Arts and Performing Arts ,05 social sciences ,0211 other engineering and technologies ,Socialist mode of production ,050801 communication & media studies ,021107 urban & regional planning ,02 engineering and technology ,0508 media and communications ,Economy ,Urban planning ,Political science ,Architecture ,Soviet union - Abstract
This special issue brings together five articles focusing on architecture and urban planning in the Soviet Union (and in one case, its export to Afghanistan) from the 1960s to the 1980s, in the per...
- Published
- 2019
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