TY  - JOUR
AU  - Jantsch, Michael F.
AU  - Quattrone, Alessandro
AU  - O'Connell, Mary
AU  - Helm, Mark
AU  - Frye, Michaela
AU  - Macias-Gonzales, Manuel
AU  - Ohman, Marie
AU  - Ameres, Stefan
AU  - Willems, Luc
AU  - Fuks, Francois
AU  - Oulas, Anastasis
AU  - Vanacova, Stepanka
AU  - Nielsen, Henrik
AU  - Bousquet-Antonelli, Cecile
AU  - Motorin, Yuri
AU  - Roignant, Jean-Yves
AU  - Balatsos, Nikolaos
AU  - Dinnyes, Andras
AU  - Baranov, Pavel
AU  - Kelly, Vincent
AU  - Lamm, Ayelet
AU  - Rechavi, Gideon
AU  - Pelizzola, Mattia
AU  - Liepins, Janis
AU  - Holodnuka Kholodnyuk, Irina
AU  - Zammit, Vanessa
AU  - Ayers, Duncan
AU  - Drablos, Finn
AU  - Dahl, John Arne
AU  - Bujnicki, Janusz
AU  - Jeronimo, Carmen
AU  - Almeida, Raquel
AU  - Neagu, Monica
AU  - Costache, Marieta
AU  - Banković, Jasna
AU  - Banović, Bojana
AU  - Kyselovic, Jan
AU  - Valor, Luis Miguel
AU  - Selbert, Stefan
AU  - Pir, Pinar
AU  - Demircan, Turan
AU  - Cowling, Victoria
AU  - Schäfer, Matthias
AU  - Rossmanith, Walter
AU  - Lafontaine, Denis
AU  - David, Alexandre
AU  - Carre, Clement
AU  - Lyko, Frank
AU  - Schaffrath, Raffael
AU  - Schwartz, Schraga
AU  - Verdel, Andre
AU  - Klungland, Arne
AU  - Purta, Elzbieta
AU  - Timotijevic, Gordana
AU  - Cardona, Fernando
AU  - Davalos, Alberto
AU  - Ballana, Ester
AU  - O Carroll, Donal
AU  - Ule, Jernej
AU  - Fray, Rupert
PY  - 2018
UR  - https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1460996
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3063
AB  - The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.
T2  - RNA Biology
T1  - Positioning Europe for the EPITRANSCRIPTOMICS challenge.
DO  - 10.1080/15476286.2018.1460996
ER  - 

@article{
author = "Jantsch, Michael F. and Quattrone, Alessandro and O'Connell, Mary and Helm, Mark and Frye, Michaela and Macias-Gonzales, Manuel and Ohman, Marie and Ameres, Stefan and Willems, Luc and Fuks, Francois and Oulas, Anastasis and Vanacova, Stepanka and Nielsen, Henrik and Bousquet-Antonelli, Cecile and Motorin, Yuri and Roignant, Jean-Yves and Balatsos, Nikolaos and Dinnyes, Andras and Baranov, Pavel and Kelly, Vincent and Lamm, Ayelet and Rechavi, Gideon and Pelizzola, Mattia and Liepins, Janis and Holodnuka Kholodnyuk, Irina and Zammit, Vanessa and Ayers, Duncan and Drablos, Finn and Dahl, John Arne and Bujnicki, Janusz and Jeronimo, Carmen and Almeida, Raquel and Neagu, Monica and Costache, Marieta and Banković, Jasna and Banović, Bojana and Kyselovic, Jan and Valor, Luis Miguel and Selbert, Stefan and Pir, Pinar and Demircan, Turan and Cowling, Victoria and Schäfer, Matthias and Rossmanith, Walter and Lafontaine, Denis and David, Alexandre and Carre, Clement and Lyko, Frank and Schaffrath, Raffael and Schwartz, Schraga and Verdel, Andre and Klungland, Arne and Purta, Elzbieta and Timotijevic, Gordana and Cardona, Fernando and Davalos, Alberto and Ballana, Ester and O Carroll, Donal and Ule, Jernej and Fray, Rupert",
year = "2018",
abstract = "The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.",
journal = "RNA Biology",
title = "Positioning Europe for the EPITRANSCRIPTOMICS challenge.",
doi = "10.1080/15476286.2018.1460996"
}

Jantsch, M. F., Quattrone, A., O'Connell, M., Helm, M., Frye, M., Macias-Gonzales, M., Ohman, M., Ameres, S., Willems, L., Fuks, F., Oulas, A., Vanacova, S., Nielsen, H., Bousquet-Antonelli, C., Motorin, Y., Roignant, J., Balatsos, N., Dinnyes, A., Baranov, P., Kelly, V., Lamm, A., Rechavi, G., Pelizzola, M., Liepins, J., Holodnuka Kholodnyuk, I., Zammit, V., Ayers, D., Drablos, F., Dahl, J. A., Bujnicki, J., Jeronimo, C., Almeida, R., Neagu, M., Costache, M., Banković, J., Banović, B., Kyselovic, J., Valor, L. M., Selbert, S., Pir, P., Demircan, T., Cowling, V., Schäfer, M., Rossmanith, W., Lafontaine, D., David, A., Carre, C., Lyko, F., Schaffrath, R., Schwartz, S., Verdel, A., Klungland, A., Purta, E., Timotijevic, G., Cardona, F., Davalos, A., Ballana, E., O Carroll, D., Ule, J.,& Fray, R.. (2018). Positioning Europe for the EPITRANSCRIPTOMICS challenge.. in RNA Biology.
https://doi.org/10.1080/15476286.2018.1460996

Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant J, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Banković J, Banović B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R. Positioning Europe for the EPITRANSCRIPTOMICS challenge.. in RNA Biology. 2018;.
doi:10.1080/15476286.2018.1460996 .

Jantsch, Michael F., Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Holodnuka Kholodnyuk, Irina, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Banković, Jasna, Banović, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schäfer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijevic, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O Carroll, Donal, Ule, Jernej, Fray, Rupert, "Positioning Europe for the EPITRANSCRIPTOMICS challenge." in RNA Biology (2018),
https://doi.org/10.1080/15476286.2018.1460996 . .

TY  - CONF
AU  - Banović, Bojana
AU  - Dinić, Svetlana
AU  - Vidaković, Melita
AU  - Miljuš Đukić, Jovanka
PY  - 2014
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6317
AB  - Common buckwheat (Fagopyrum esculentum Moench) is a self-incompatible dicot species with two morphologically different flower types: thrum (shorter style, longer anthers, larger pollen grains) and pin (longer style, shorter anthers, smaller pollen grains). In this species fertilization is allowed only between flowers of different morphology (compatible pollination), while it is prevented between flowers of the same morphology (incompatible pollination) through self-incompatibility (SI). Two flower morphs have different expression site of the SI response: in thrum pistil at the junction of stigma and style, and in pin pistil at 2/3 of style’s length. It is well documented that SI response includes various protein-protein interactions in other studied plant SI species, but so far there are no such reports for buckwheat. The aim of our study was to track and compare changes in proteome profiles of thrum and pin pistils’ upon their incompatible and compatible pollination. Total proteins extracted from non-pollinated, incompatibly and compatibly pollinated thrum and pin pistils were separated by 2D-PAGE and analyzed using Image Master 2D Platinum software v6.0. In each sample, proteome profiles revealed distribution over a wide mass range (10-130 kDa), with the prevalence of acidic to neutral proteins (pI 3.5-7) and only a few basic proteins (pI 7.5-9). The most abundant proteins were those shared by two morphs, which were present independently of pollination type (incompatible/compatible) (c. 90-95% of detected spots per sample). Proteins specific for morph and pollination type were also discovered (c. 5-10% of detected spots per sample) and will be identified by MS analysis.
PB  - International Association of Sexua Plant Reproduction Research
C3  - 23rd International Congress on Sexual Plant Reproduction: Seeds for the future; 2014 Jul 13-18; Porto, Portugal
T1  - Comparative 2D-proteome analyses of non-pollinated, incompatibly and compatibly pollinated thrum and pin pistils of common buckwheat
SP  - 148
EP  - 148
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6317
ER  - 

@conference{
author = "Banović, Bojana and Dinić, Svetlana and Vidaković, Melita and Miljuš Đukić, Jovanka",
year = "2014",
abstract = "Common buckwheat (Fagopyrum esculentum Moench) is a self-incompatible dicot species with two morphologically different flower types: thrum (shorter style, longer anthers, larger pollen grains) and pin (longer style, shorter anthers, smaller pollen grains). In this species fertilization is allowed only between flowers of different morphology (compatible pollination), while it is prevented between flowers of the same morphology (incompatible pollination) through self-incompatibility (SI). Two flower morphs have different expression site of the SI response: in thrum pistil at the junction of stigma and style, and in pin pistil at 2/3 of style’s length. It is well documented that SI response includes various protein-protein interactions in other studied plant SI species, but so far there are no such reports for buckwheat. The aim of our study was to track and compare changes in proteome profiles of thrum and pin pistils’ upon their incompatible and compatible pollination. Total proteins extracted from non-pollinated, incompatibly and compatibly pollinated thrum and pin pistils were separated by 2D-PAGE and analyzed using Image Master 2D Platinum software v6.0. In each sample, proteome profiles revealed distribution over a wide mass range (10-130 kDa), with the prevalence of acidic to neutral proteins (pI 3.5-7) and only a few basic proteins (pI 7.5-9). The most abundant proteins were those shared by two morphs, which were present independently of pollination type (incompatible/compatible) (c. 90-95% of detected spots per sample). Proteins specific for morph and pollination type were also discovered (c. 5-10% of detected spots per sample) and will be identified by MS analysis.",
publisher = "International Association of Sexua Plant Reproduction Research",
journal = "23rd International Congress on Sexual Plant Reproduction: Seeds for the future; 2014 Jul 13-18; Porto, Portugal",
title = "Comparative 2D-proteome analyses of non-pollinated, incompatibly and compatibly pollinated thrum and pin pistils of common buckwheat",
pages = "148-148",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6317"
}

Banović, B., Dinić, S., Vidaković, M.,& Miljuš Đukić, J.. (2014). Comparative 2D-proteome analyses of non-pollinated, incompatibly and compatibly pollinated thrum and pin pistils of common buckwheat. in 23rd International Congress on Sexual Plant Reproduction: Seeds for the future; 2014 Jul 13-18; Porto, Portugal
International Association of Sexua Plant Reproduction Research., 148-148.
https://hdl.handle.net/21.15107/rcub_ibiss_6317

Banović B, Dinić S, Vidaković M, Miljuš Đukić J. Comparative 2D-proteome analyses of non-pollinated, incompatibly and compatibly pollinated thrum and pin pistils of common buckwheat. in 23rd International Congress on Sexual Plant Reproduction: Seeds for the future; 2014 Jul 13-18; Porto, Portugal. 2014;:148-148.
https://hdl.handle.net/21.15107/rcub_ibiss_6317 .

Banović, Bojana, Dinić, Svetlana, Vidaković, Melita, Miljuš Đukić, Jovanka, "Comparative 2D-proteome analyses of non-pollinated, incompatibly and compatibly pollinated thrum and pin pistils of common buckwheat" in 23rd International Congress on Sexual Plant Reproduction: Seeds for the future; 2014 Jul 13-18; Porto, Portugal (2014):148-148,
https://hdl.handle.net/21.15107/rcub_ibiss_6317 .

TY  - JOUR
AU  - Nikolić, Radomirka R
AU  - Zdravković-Korać, Snežana
AU  - Ninković, Slavica
AU  - Dragićević, Milan
AU  - Miljuš-Đukić, Jovanka D.
AU  - Banović, Bojana
AU  - Bohanec, Borut
AU  - Savić, Jelena
AU  - Banjac, Nevena
PY  - 2013
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/957
AB  - Resistance to the non-selective herbicide dl-phosphinothricin (PPT) was introduced into commercial Lotus corniculatus cv. Bokor by co-cultivation of cotyledons with Agrobacterium tumefaciensAGL1 harbouring the binary vector pDM805 which contains the bialaphos resistance gene (bar) from Streptomyces hygroscopicus encoding phosphinothricin acetyltransferase (PAT) and the uidA gene encoding -glucuronidase. The half-cotyledon explants were precultured on regeneration Murashige and Skoog's (MS) medium supplemented with 6-benzyladenine (BA) and 1-naphthaleneacetic acid (NAA) at 0.5mgL(-1) each, 3days prior to infection. Upon co-cultivation, the explants were cultured on PPT-free regeneration medium for 10days, and then subcultured on regeneration/selection media with increasing PPT concentrations (5-7mgL(-1)) for about 18weeks. Out of 480 initially co-cultivated explants, 272 regenerated shoots survived the entire PPT selection procedure. Resistant shoots were grown further, multiplied by tillering that was additionally promoted by PPT and rooted on hormone-free MS medium containing 5mgL(-1) PPT. Established shoot cultures, continuously maintained on the same medium, have preserved PPT resistance up to now (more than 2years). Transformed plants assessed in vitro and in a greenhouse were tolerant to the herbicide PPT at 300mgL(-1) equivalent to more than twofold the recommended field dosage for weed eradication. Applied PPT treatment did not affect the activities of glutamine synthetase (GS; EC 6.3.1.2) and NADH-dependent glutamate dehydrogenase (NADH-GDH; EC 1.4.1.2) in transformed plants. However, PPT did increase the mobility of glutamine synthetase isoforms GS1 and GS2 as well as the inhibition of an additional high mobility GS (hmGS) activity. In untransformed plants, PPT treatment reduced total GS activity by 4.4-fold while contrary the activity of NADH-GDH was increased by ninefold. All transformed herbicide-resistant plants were phenotypically normal and exhibited genomic stability, as were the untransformed plants analysed by flow cytometry. Under greenhouse conditions, they grew to maturity, flowered and set seeds. Stable integration and expression of the bar gene in T0 and T1 plants were confirmed by Southern and Western blot analysis, while integration of the reporter uidA gene did not occur. The bar gene was inherited in a Mendelian fashion by the progeny, as detected by PPT resistance. The production of PPT-resistant plants may have significant practical applications in weed control in fields of L. corniculatus.
T2  - Annals of Applied Biology
T1  - Fertile transgenic Lotus corniculatus resistant to the non-selective herbicide phosphinothricin
IS  - 3
VL  - 163
DO  - 10.1111/aab.12071
SP  - 247
EP  - 493
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_957
ER  - 

@article{
author = "Nikolić, Radomirka R and Zdravković-Korać, Snežana and Ninković, Slavica and Dragićević, Milan and Miljuš-Đukić, Jovanka D. and Banović, Bojana and Bohanec, Borut and Savić, Jelena and Banjac, Nevena",
year = "2013",
abstract = "Resistance to the non-selective herbicide dl-phosphinothricin (PPT) was introduced into commercial Lotus corniculatus cv. Bokor by co-cultivation of cotyledons with Agrobacterium tumefaciensAGL1 harbouring the binary vector pDM805 which contains the bialaphos resistance gene (bar) from Streptomyces hygroscopicus encoding phosphinothricin acetyltransferase (PAT) and the uidA gene encoding -glucuronidase. The half-cotyledon explants were precultured on regeneration Murashige and Skoog's (MS) medium supplemented with 6-benzyladenine (BA) and 1-naphthaleneacetic acid (NAA) at 0.5mgL(-1) each, 3days prior to infection. Upon co-cultivation, the explants were cultured on PPT-free regeneration medium for 10days, and then subcultured on regeneration/selection media with increasing PPT concentrations (5-7mgL(-1)) for about 18weeks. Out of 480 initially co-cultivated explants, 272 regenerated shoots survived the entire PPT selection procedure. Resistant shoots were grown further, multiplied by tillering that was additionally promoted by PPT and rooted on hormone-free MS medium containing 5mgL(-1) PPT. Established shoot cultures, continuously maintained on the same medium, have preserved PPT resistance up to now (more than 2years). Transformed plants assessed in vitro and in a greenhouse were tolerant to the herbicide PPT at 300mgL(-1) equivalent to more than twofold the recommended field dosage for weed eradication. Applied PPT treatment did not affect the activities of glutamine synthetase (GS; EC 6.3.1.2) and NADH-dependent glutamate dehydrogenase (NADH-GDH; EC 1.4.1.2) in transformed plants. However, PPT did increase the mobility of glutamine synthetase isoforms GS1 and GS2 as well as the inhibition of an additional high mobility GS (hmGS) activity. In untransformed plants, PPT treatment reduced total GS activity by 4.4-fold while contrary the activity of NADH-GDH was increased by ninefold. All transformed herbicide-resistant plants were phenotypically normal and exhibited genomic stability, as were the untransformed plants analysed by flow cytometry. Under greenhouse conditions, they grew to maturity, flowered and set seeds. Stable integration and expression of the bar gene in T0 and T1 plants were confirmed by Southern and Western blot analysis, while integration of the reporter uidA gene did not occur. The bar gene was inherited in a Mendelian fashion by the progeny, as detected by PPT resistance. The production of PPT-resistant plants may have significant practical applications in weed control in fields of L. corniculatus.",
journal = "Annals of Applied Biology",
title = "Fertile transgenic Lotus corniculatus resistant to the non-selective herbicide phosphinothricin",
number = "3",
volume = "163",
doi = "10.1111/aab.12071",
pages = "247-493",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_957"
}

Nikolić, R. R., Zdravković-Korać, S., Ninković, S., Dragićević, M., Miljuš-Đukić, J. D., Banović, B., Bohanec, B., Savić, J.,& Banjac, N.. (2013). Fertile transgenic Lotus corniculatus resistant to the non-selective herbicide phosphinothricin. in Annals of Applied Biology, 163(3), 247-493.
https://doi.org/10.1111/aab.12071
https://hdl.handle.net/21.15107/rcub_ibiss_957

Nikolić RR, Zdravković-Korać S, Ninković S, Dragićević M, Miljuš-Đukić JD, Banović B, Bohanec B, Savić J, Banjac N. Fertile transgenic Lotus corniculatus resistant to the non-selective herbicide phosphinothricin. in Annals of Applied Biology. 2013;163(3):247-493.
doi:10.1111/aab.12071
https://hdl.handle.net/21.15107/rcub_ibiss_957 .

Nikolić, Radomirka R, Zdravković-Korać, Snežana, Ninković, Slavica, Dragićević, Milan, Miljuš-Đukić, Jovanka D., Banović, Bojana, Bohanec, Borut, Savić, Jelena, Banjac, Nevena, "Fertile transgenic Lotus corniculatus resistant to the non-selective herbicide phosphinothricin" in Annals of Applied Biology, 163, no. 3 (2013):247-493,
https://doi.org/10.1111/aab.12071 .,
https://hdl.handle.net/21.15107/rcub_ibiss_957 .