TY  - JOUR
AU  - Marković, Marija
AU  - Trifunović-Momčilov, Milana
AU  - Radulović, Olga
AU  - Paunović, Danijela
AU  - Antonić Reljin, Dragana
AU  - Jevremović, Slađana
AU  - Uzelac, Branka
PY  - 2024
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6522
AB  - The genus Fritillaria is characterized by the production of alkaloids, primarily of the isosteroidal type. The aim of this preliminary study was to perform a histolocalization screening aimed at revealing the presence of alkaloids in the bulbs of F. meleagris, cultured in vitro under different growth regimes and at different developmental stages, as a powerful tool to identify preferable in vitro plant material for alkaloid isolation. Histochemical localization of alkaloids was performed using Wagner’s and Dragendorff’s reagents in fresh sections of bulbs cultured at 24 °C or 7 °C for 4 weeks, as well as those cultured at 24 °C following the 4-week chilling treatment, which were sampled at the beginning of sprouting. A positive reaction was observed with both reagents and was particularly intense in cold-treated bulbs. Alkaloids were mainly distributed in the bulbs and partly in the sprouts of the in vitro grown F. meleagris. The most intense staining, indicative of high alkaloid content, was observed in the bulb scales of pre-chilled bulbs that sprouted at 24 °C, rendering them preferable as in vitro plant material for alkaloid isolation. The results suggest that alkaloid production in the bulbs of F. meleagris can be improved by manipulating growth in the microenvironment of in vitro cultures, in order to meet the increasing industrial demand for medicinally or commercially important metabolites used as traditional medicines and herbal remedies.
PB  - Basel : MDPI
T2  - Horticulturae
T1  - Histochemical Localization of Alkaloids in the Bulbs of In Vitro-Regenerated Snake’s Head Fritillary (Fritillaria meleagris L.): The Effect of a Temperature Regime
IS  - 1
VL  - 10
DO  - 10.3390/horticulturae10010017
SP  - 17
ER  - 

@article{
author = "Marković, Marija and Trifunović-Momčilov, Milana and Radulović, Olga and Paunović, Danijela and Antonić Reljin, Dragana and Jevremović, Slađana and Uzelac, Branka",
year = "2024",
abstract = "The genus Fritillaria is characterized by the production of alkaloids, primarily of the isosteroidal type. The aim of this preliminary study was to perform a histolocalization screening aimed at revealing the presence of alkaloids in the bulbs of F. meleagris, cultured in vitro under different growth regimes and at different developmental stages, as a powerful tool to identify preferable in vitro plant material for alkaloid isolation. Histochemical localization of alkaloids was performed using Wagner’s and Dragendorff’s reagents in fresh sections of bulbs cultured at 24 °C or 7 °C for 4 weeks, as well as those cultured at 24 °C following the 4-week chilling treatment, which were sampled at the beginning of sprouting. A positive reaction was observed with both reagents and was particularly intense in cold-treated bulbs. Alkaloids were mainly distributed in the bulbs and partly in the sprouts of the in vitro grown F. meleagris. The most intense staining, indicative of high alkaloid content, was observed in the bulb scales of pre-chilled bulbs that sprouted at 24 °C, rendering them preferable as in vitro plant material for alkaloid isolation. The results suggest that alkaloid production in the bulbs of F. meleagris can be improved by manipulating growth in the microenvironment of in vitro cultures, in order to meet the increasing industrial demand for medicinally or commercially important metabolites used as traditional medicines and herbal remedies.",
publisher = "Basel : MDPI",
journal = "Horticulturae",
title = "Histochemical Localization of Alkaloids in the Bulbs of In Vitro-Regenerated Snake’s Head Fritillary (Fritillaria meleagris L.): The Effect of a Temperature Regime",
number = "1",
volume = "10",
doi = "10.3390/horticulturae10010017",
pages = "17"
}

Marković, M., Trifunović-Momčilov, M., Radulović, O., Paunović, D., Antonić Reljin, D., Jevremović, S.,& Uzelac, B.. (2024). Histochemical Localization of Alkaloids in the Bulbs of In Vitro-Regenerated Snake’s Head Fritillary (Fritillaria meleagris L.): The Effect of a Temperature Regime. in Horticulturae
Basel : MDPI., 10(1), 17.
https://doi.org/10.3390/horticulturae10010017

Marković M, Trifunović-Momčilov M, Radulović O, Paunović D, Antonić Reljin D, Jevremović S, Uzelac B. Histochemical Localization of Alkaloids in the Bulbs of In Vitro-Regenerated Snake’s Head Fritillary (Fritillaria meleagris L.): The Effect of a Temperature Regime. in Horticulturae. 2024;10(1):17.
doi:10.3390/horticulturae10010017 .

Marković, Marija, Trifunović-Momčilov, Milana, Radulović, Olga, Paunović, Danijela, Antonić Reljin, Dragana, Jevremović, Slađana, Uzelac, Branka, "Histochemical Localization of Alkaloids in the Bulbs of In Vitro-Regenerated Snake’s Head Fritillary (Fritillaria meleagris L.): The Effect of a Temperature Regime" in Horticulturae, 10, no. 1 (2024):17,
https://doi.org/10.3390/horticulturae10010017 . .

TY  - JOUR
AU  - Marković, Marija
AU  - Trifunović-Momčilov, Milana
AU  - Radulović, Olga
AU  - Paunović, Danijela
AU  - Antonić Reljin, Dragana
AU  - Uzelac, Branka
AU  - Subotić, Angelina
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6089
AB  - Fritillaria meleagris is a horticulturally and medicinally valuable bulbous plant that requires a period of low temperatures for proper growth and flowering. Since conventional methods of propagation are ineffective and very slow, tissue culture techniques offer an integrated approach to mass production of this valuable geophyte. In this study, we investigated the effects of various auxin–cytokinin combinations on different morphogenetic pathways in bulb scale culture. Bulbs obtained in vitro were cut longitudinally, and bulb scales were cultured for four weeks at 7 °C on MS medium supplemented with 6-benzylaminopurine (BAP) in combination with 2,4-dichlorophenoxyacetic acid (2,4-D) or α-naphthaleneacetic acid (NAA) at different concentrations in order to investigate the influence of plant growth regulators (PGRs) on different morphogenetic responses. Regeneration percentage, number of shoots per explant, shoot length, number of bulbs and number of somatic embryos were monitored weekly. After chilling, bulb scales were transferred to 24 °C, and all parameters were recorded again. Low PGR concentrations were very effective for shoot multiplication, yielding up to 5.5 shoots per explant. 2,4-D (at 2 mg/L) in combination with low BAP (0.25 mg/L) produced the highest number of bulbs (11.00 ± 0.00), while PGR-free medium was extremely effective in somatic embryo formation (13.50 ± 2.90). Detached somatic embryos and bulblets continued to grow and develop on fresh PGR-free medium. We present data demonstrating that low auxin–cytokinin concentrations and PGR-free medium provide an effective method for a combined morphogenetic pathway in F. meleagris that is suitable for large-scale propagation.
PB  - Basel : MDPI
T2  - Horticulturae
T1  - The Effects of Different Auxin–Cytokinin Combinations on Morphogenesis of Fritillaria meleagris Using Bulb Scale Sections In Vitro
IS  - 8
VL  - 9
DO  - 10.3390/horticulturae9080910
SP  - 910
ER  - 

@article{
author = "Marković, Marija and Trifunović-Momčilov, Milana and Radulović, Olga and Paunović, Danijela and Antonić Reljin, Dragana and Uzelac, Branka and Subotić, Angelina",
year = "2023",
abstract = "Fritillaria meleagris is a horticulturally and medicinally valuable bulbous plant that requires a period of low temperatures for proper growth and flowering. Since conventional methods of propagation are ineffective and very slow, tissue culture techniques offer an integrated approach to mass production of this valuable geophyte. In this study, we investigated the effects of various auxin–cytokinin combinations on different morphogenetic pathways in bulb scale culture. Bulbs obtained in vitro were cut longitudinally, and bulb scales were cultured for four weeks at 7 °C on MS medium supplemented with 6-benzylaminopurine (BAP) in combination with 2,4-dichlorophenoxyacetic acid (2,4-D) or α-naphthaleneacetic acid (NAA) at different concentrations in order to investigate the influence of plant growth regulators (PGRs) on different morphogenetic responses. Regeneration percentage, number of shoots per explant, shoot length, number of bulbs and number of somatic embryos were monitored weekly. After chilling, bulb scales were transferred to 24 °C, and all parameters were recorded again. Low PGR concentrations were very effective for shoot multiplication, yielding up to 5.5 shoots per explant. 2,4-D (at 2 mg/L) in combination with low BAP (0.25 mg/L) produced the highest number of bulbs (11.00 ± 0.00), while PGR-free medium was extremely effective in somatic embryo formation (13.50 ± 2.90). Detached somatic embryos and bulblets continued to grow and develop on fresh PGR-free medium. We present data demonstrating that low auxin–cytokinin concentrations and PGR-free medium provide an effective method for a combined morphogenetic pathway in F. meleagris that is suitable for large-scale propagation.",
publisher = "Basel : MDPI",
journal = "Horticulturae",
title = "The Effects of Different Auxin–Cytokinin Combinations on Morphogenesis of Fritillaria meleagris Using Bulb Scale Sections In Vitro",
number = "8",
volume = "9",
doi = "10.3390/horticulturae9080910",
pages = "910"
}

Marković, M., Trifunović-Momčilov, M., Radulović, O., Paunović, D., Antonić Reljin, D., Uzelac, B.,& Subotić, A.. (2023). The Effects of Different Auxin–Cytokinin Combinations on Morphogenesis of Fritillaria meleagris Using Bulb Scale Sections In Vitro. in Horticulturae
Basel : MDPI., 9(8), 910.
https://doi.org/10.3390/horticulturae9080910

Marković M, Trifunović-Momčilov M, Radulović O, Paunović D, Antonić Reljin D, Uzelac B, Subotić A. The Effects of Different Auxin–Cytokinin Combinations on Morphogenesis of Fritillaria meleagris Using Bulb Scale Sections In Vitro. in Horticulturae. 2023;9(8):910.
doi:10.3390/horticulturae9080910 .

Marković, Marija, Trifunović-Momčilov, Milana, Radulović, Olga, Paunović, Danijela, Antonić Reljin, Dragana, Uzelac, Branka, Subotić, Angelina, "The Effects of Different Auxin–Cytokinin Combinations on Morphogenesis of Fritillaria meleagris Using Bulb Scale Sections In Vitro" in Horticulturae, 9, no. 8 (2023):910,
https://doi.org/10.3390/horticulturae9080910 . .

TY  - THES
AU  - Paunović, Danijela
PY  - 2022
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5019
AB  - Arabinogalaktanski proteini (AGP) su ekstenzivno glikozilovani proteini ćelijskog zida i predstavljaju podklasu O-glikozilovanih glikoproteina bogatih hidroksiprolinom (HRGP). Odlikuje ih visoka raznolikost primarne strukture, velika familija gena koja ih kodira, kao i širok spektar uloga tokom rastenja i razvića biljaka. AGP su proteini sa neuređenom strukturom što otežava njihovu identifikaciju na osnovu homologije sekvenci. Sa ciljem poboljšanja metodologije za identifikaciju i analizu HRGP sekvenci u sklopu ove doktorske disertacije razvijen je pristup zasnovan na mašinskom učenju. Ovaj pristup koristi glavnu odliku HRGP, a to je prisustvo nekarakteristične aminokiseline hidroksiprolina. Model za predviđanje verovatnoće hidroksilacije prolina na osnovu lokalne sekvence proteina inkorporiran je u ragp R paket uz brojne druge alate koji omogućavaju analize proteinskih sekvenci kao što su: klasifikacija HRGP sekvenci, fleksibilna pretraga karakterističnih motiva, efikasna komunikacija sa serverima za predviđanje N-terminalne signalne sekvence, mesta dodavanja glikozil-fosfatidilinozitolnog sidra, određivanje položaja neuređenih regiona i anotaciju domena u sekvencama. Navedena metodologija omogućava prilagodljivu identifikaciju sekvenci pri kojoj izbor nekoliko parametara utiče na rigoroznost procesa, a time i broj identifikovanih sekvenci. Navedeni softver omogućava efikasnu identifikaciju HRGP sekvenci u celim biljnim proteomima što predstavlja preduslov za njihovo dalje ispitivanje. Kičicu (Centaurium erythraea) karakteriše velika razvojna plastičnost i snažan morfogenetski potencijal, što je čini pogodnim model organizmom za istraživanja u razvojnoj biologiji. AGP su identifikovani kao značajan biohemijski marker somatske embriogeneze i organogeneze kičice i kao takvi mogu biti značajni za proces regeneracije kako biljaka gajenih u uslovima in vitro, tako i onih u prirodi. Povrede predstavljaju sastavni deo manipulacije biljnim tkivom in vitro i mogu indukovati morfogenetske procese. Odgovor biljke indukovan Yariv reagensom, koji specifično precipituje AGP, najsličniji je odgovoru indukovanom mehaničkim povredama biljnog tkiva. Može se pretpostaviti da postoji veza između procesa koji se odigravaju u i na ćeliji, a koji su inicirani mehaničkim povredama ili primenom Yariv reagensa kao i tokom indukcije somatske embriogeneze i organogeneze kičice. Nedavno sekvenciran transkriptom kičice uz razvoj ragp R paketa omogućio je identifikaciju velikog broja HRGP i AGP sekvenci kičice. Od identifikovanih sekvenci odabrano je osamnaest predstavnika za ispitivanje ekspresije u različitim uslovima. Ekspresija odabranih gena praćena je: a) 48 h nakon mehaničke povrede lista i korena biljaka kičice gajenih u uslovima in vitro b) u eksplantatima lista i korena kičice gajenih na različitim koncentracijama Yariv reagensa c) u različitim uzorcima biljaka gajenih in vitro, biljaka iz prirode i iz različitih morfogenetskih procesa kičice (somatske embriogeneze i organogeneze). Od odabranih osamnaest gena, CeAGp6, koji kodira kratak AG peptid, bio je izraženo indukovan nakon mehaničke povrede lista, a reprimiran nakon povrede korena. Moguće je da ovaj AG peptid uključen u određen tip prenosa signala nakon povrede biljnog tkiva. Pored njega CeFLA1, koji je pokazao povećanje ekspresije tokom 48 h nakon povrede lista, a indukovan je i u embriogenom kalusu, mogao bi biti deo mreže koja povezuje povrede i somatsku embriogenezu.
AB  - Arabinogalactan proteins (AGPs) are extensively glycosylated cell wall proteins belonging to the super family of O-glycosylated hydroxyproline-rich glycoproteins (HRGPs). They are characterized by a high diversity of the primary structure, they are encoded by a large gene family and are associated with a wide array of physiological roles in plant growth and development. AGPs are intrinsically disordered proteins which hinders their homology-based identification. In order to improve the methodology for identification and analysis of HRGP sequences, a new machine learning based approach was developed as part of this thesis. This approach exploits the main feature of HRGPs, the presence of the uncharacteristic amino acid hydroxyproline. A model for predicting proline hydroxylation probability based on local protein sequence has been incorporated into the ragp R package along with a number of diverse tools that allow the analysis of protein sequences such as: classification of HRGPs sequences, flexible scan for characteristic motifs, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites, disordered regions and domain annotation. The implemented pipeline enables adaptable identification of sequences where the choice of several parameters affects the stringency of the process and thus the number of sequences identified. This software allows efficient identification of HRGPs sequences in whole plant proteomes, which is a prerequisite for their further study. Common centaury (Centaurium erythraea) is characterized by an exceptional developmental plasticity and strong morphogenetic potential, which makes it a suitable model organism for developmental biology studies. AGPs have been identified as a significant factor during somatic embryogenesis and organogenesis of common centaury, and as such can be important for the regeneration process in both plants grown in vitro and plants from nature. Mechanical wounding is an integral part of plant tissue manipulation in vitro and can induce morphogenetic processes. The plant response induced by Yariv reagent, which specifically precipitates AGPs, is most similar to the response induced by mechanical wounding of plant tissue. It can be assumed that there is a connection between the processes that take place in and on the cell, which are initiated by mechanical wounding, application of Yariv reagents and during the induction of somatic embryogenesis and organogenesis. The recently sequenced C. erythraea transcriptome combined with the development of ragp R package allowed the identification of a large number of C. erythraea HRGP and AGP sequences. Eighteen representatives were selected from the identified sequences for expression analyses in different experimental conditions. The expression of selected genes was recorded: a) 48h following leaf and root mechanical wounding in vitro b) in leaf and root explants cultivated on different concentrations of Yariv reagent in medium c) in samples from plants cultivated in vitro, plants from nature and from different morphogenetic processes (somatic embryogenesis i organogenesis). Among the selected eighteen genes, CeAGp6, which encodes a short AG peptide, was significantly induced after mechanical wounding of leaf, and down-regulated after mechanical wounding of root. It is possible that this AG peptide is involved in some type of signal transduction after plant tissue wounding. CeFLA1 which showed a clear trend of increasing expression over time after leaf wounding, and is induced in embryogenic callus, could be part of a network linking wounding with somatic embryogenesis.
PB  - Belgrade: Faculty of Biology, University of Belgrade
T2  - Faculty of Biology, University of Belgrade
T1  - Identifikacija AGP gena kičice (Centaurium erythraea, Gentianaceae) i praćenje njihove ekspresije u odgovoru na mehaničke povrede biljnog tkiva gajenog in vitro
T1  - Identification of AGP genes in centaury (Centaurium erythraea, Gentianaceae) and monitoring of their expression in response to tissue mechanical wounding in vitro
SP  - 1
EP  - 117
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5019
ER  - 

@phdthesis{
author = "Paunović, Danijela",
year = "2022",
abstract = "Arabinogalaktanski proteini (AGP) su ekstenzivno glikozilovani proteini ćelijskog zida i predstavljaju podklasu O-glikozilovanih glikoproteina bogatih hidroksiprolinom (HRGP). Odlikuje ih visoka raznolikost primarne strukture, velika familija gena koja ih kodira, kao i širok spektar uloga tokom rastenja i razvića biljaka. AGP su proteini sa neuređenom strukturom što otežava njihovu identifikaciju na osnovu homologije sekvenci. Sa ciljem poboljšanja metodologije za identifikaciju i analizu HRGP sekvenci u sklopu ove doktorske disertacije razvijen je pristup zasnovan na mašinskom učenju. Ovaj pristup koristi glavnu odliku HRGP, a to je prisustvo nekarakteristične aminokiseline hidroksiprolina. Model za predviđanje verovatnoće hidroksilacije prolina na osnovu lokalne sekvence proteina inkorporiran je u ragp R paket uz brojne druge alate koji omogućavaju analize proteinskih sekvenci kao što su: klasifikacija HRGP sekvenci, fleksibilna pretraga karakterističnih motiva, efikasna komunikacija sa serverima za predviđanje N-terminalne signalne sekvence, mesta dodavanja glikozil-fosfatidilinozitolnog sidra, određivanje položaja neuređenih regiona i anotaciju domena u sekvencama. Navedena metodologija omogućava prilagodljivu identifikaciju sekvenci pri kojoj izbor nekoliko parametara utiče na rigoroznost procesa, a time i broj identifikovanih sekvenci. Navedeni softver omogućava efikasnu identifikaciju HRGP sekvenci u celim biljnim proteomima što predstavlja preduslov za njihovo dalje ispitivanje. Kičicu (Centaurium erythraea) karakteriše velika razvojna plastičnost i snažan morfogenetski potencijal, što je čini pogodnim model organizmom za istraživanja u razvojnoj biologiji. AGP su identifikovani kao značajan biohemijski marker somatske embriogeneze i organogeneze kičice i kao takvi mogu biti značajni za proces regeneracije kako biljaka gajenih u uslovima in vitro, tako i onih u prirodi. Povrede predstavljaju sastavni deo manipulacije biljnim tkivom in vitro i mogu indukovati morfogenetske procese. Odgovor biljke indukovan Yariv reagensom, koji specifično precipituje AGP, najsličniji je odgovoru indukovanom mehaničkim povredama biljnog tkiva. Može se pretpostaviti da postoji veza između procesa koji se odigravaju u i na ćeliji, a koji su inicirani mehaničkim povredama ili primenom Yariv reagensa kao i tokom indukcije somatske embriogeneze i organogeneze kičice. Nedavno sekvenciran transkriptom kičice uz razvoj ragp R paketa omogućio je identifikaciju velikog broja HRGP i AGP sekvenci kičice. Od identifikovanih sekvenci odabrano je osamnaest predstavnika za ispitivanje ekspresije u različitim uslovima. Ekspresija odabranih gena praćena je: a) 48 h nakon mehaničke povrede lista i korena biljaka kičice gajenih u uslovima in vitro b) u eksplantatima lista i korena kičice gajenih na različitim koncentracijama Yariv reagensa c) u različitim uzorcima biljaka gajenih in vitro, biljaka iz prirode i iz različitih morfogenetskih procesa kičice (somatske embriogeneze i organogeneze). Od odabranih osamnaest gena, CeAGp6, koji kodira kratak AG peptid, bio je izraženo indukovan nakon mehaničke povrede lista, a reprimiran nakon povrede korena. Moguće je da ovaj AG peptid uključen u određen tip prenosa signala nakon povrede biljnog tkiva. Pored njega CeFLA1, koji je pokazao povećanje ekspresije tokom 48 h nakon povrede lista, a indukovan je i u embriogenom kalusu, mogao bi biti deo mreže koja povezuje povrede i somatsku embriogenezu., Arabinogalactan proteins (AGPs) are extensively glycosylated cell wall proteins belonging to the super family of O-glycosylated hydroxyproline-rich glycoproteins (HRGPs). They are characterized by a high diversity of the primary structure, they are encoded by a large gene family and are associated with a wide array of physiological roles in plant growth and development. AGPs are intrinsically disordered proteins which hinders their homology-based identification. In order to improve the methodology for identification and analysis of HRGP sequences, a new machine learning based approach was developed as part of this thesis. This approach exploits the main feature of HRGPs, the presence of the uncharacteristic amino acid hydroxyproline. A model for predicting proline hydroxylation probability based on local protein sequence has been incorporated into the ragp R package along with a number of diverse tools that allow the analysis of protein sequences such as: classification of HRGPs sequences, flexible scan for characteristic motifs, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites, disordered regions and domain annotation. The implemented pipeline enables adaptable identification of sequences where the choice of several parameters affects the stringency of the process and thus the number of sequences identified. This software allows efficient identification of HRGPs sequences in whole plant proteomes, which is a prerequisite for their further study. Common centaury (Centaurium erythraea) is characterized by an exceptional developmental plasticity and strong morphogenetic potential, which makes it a suitable model organism for developmental biology studies. AGPs have been identified as a significant factor during somatic embryogenesis and organogenesis of common centaury, and as such can be important for the regeneration process in both plants grown in vitro and plants from nature. Mechanical wounding is an integral part of plant tissue manipulation in vitro and can induce morphogenetic processes. The plant response induced by Yariv reagent, which specifically precipitates AGPs, is most similar to the response induced by mechanical wounding of plant tissue. It can be assumed that there is a connection between the processes that take place in and on the cell, which are initiated by mechanical wounding, application of Yariv reagents and during the induction of somatic embryogenesis and organogenesis. The recently sequenced C. erythraea transcriptome combined with the development of ragp R package allowed the identification of a large number of C. erythraea HRGP and AGP sequences. Eighteen representatives were selected from the identified sequences for expression analyses in different experimental conditions. The expression of selected genes was recorded: a) 48h following leaf and root mechanical wounding in vitro b) in leaf and root explants cultivated on different concentrations of Yariv reagent in medium c) in samples from plants cultivated in vitro, plants from nature and from different morphogenetic processes (somatic embryogenesis i organogenesis). Among the selected eighteen genes, CeAGp6, which encodes a short AG peptide, was significantly induced after mechanical wounding of leaf, and down-regulated after mechanical wounding of root. It is possible that this AG peptide is involved in some type of signal transduction after plant tissue wounding. CeFLA1 which showed a clear trend of increasing expression over time after leaf wounding, and is induced in embryogenic callus, could be part of a network linking wounding with somatic embryogenesis.",
publisher = "Belgrade: Faculty of Biology, University of Belgrade",
journal = "Faculty of Biology, University of Belgrade",
title = "Identifikacija AGP gena kičice (Centaurium erythraea, Gentianaceae) i praćenje njihove ekspresije u odgovoru na mehaničke povrede biljnog tkiva gajenog in vitro, Identification of AGP genes in centaury (Centaurium erythraea, Gentianaceae) and monitoring of their expression in response to tissue mechanical wounding in vitro",
pages = "1-117",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5019"
}

Paunović, D.. (2022). Identifikacija AGP gena kičice (Centaurium erythraea, Gentianaceae) i praćenje njihove ekspresije u odgovoru na mehaničke povrede biljnog tkiva gajenog in vitro. in Faculty of Biology, University of Belgrade
Belgrade: Faculty of Biology, University of Belgrade., 1-117.
https://hdl.handle.net/21.15107/rcub_ibiss_5019

Paunović D. Identifikacija AGP gena kičice (Centaurium erythraea, Gentianaceae) i praćenje njihove ekspresije u odgovoru na mehaničke povrede biljnog tkiva gajenog in vitro. in Faculty of Biology, University of Belgrade. 2022;:1-117.
https://hdl.handle.net/21.15107/rcub_ibiss_5019 .

Paunović, Danijela, "Identifikacija AGP gena kičice (Centaurium erythraea, Gentianaceae) i praćenje njihove ekspresije u odgovoru na mehaničke povrede biljnog tkiva gajenog in vitro" in Faculty of Biology, University of Belgrade (2022):1-117,
https://hdl.handle.net/21.15107/rcub_ibiss_5019 .

TY  - JOUR
AU  - Paunović, Danijela
AU  - Ćuković, Katarina
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Trifunović-Momčilov, Milana
AU  - Subotić, Angelina
AU  - Simonović, Ana
AU  - Dragićević, Milan
PY  - 2021
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4392
AB  - Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family of O-glycosylated plant cell surface hydroxyproline-rich glycoproteins (HRGPs). HRGPs/AGPs are intrinsically disordered and not well conserved, making their homology-based mining ineffective. We have applied a recently developed pipeline for HRGP/AGP mining, ragp, which is based on machine learning prediction of proline hydroxylation, to identify HRGP sequences in centaury transcriptome and to classify them into motif and amino acid bias (MAAB) classes. AGP sequences with low AG glycomotif representation were also identified. Six members of each of the three AGP subclasses, fasciclin-like AGPs, receptor kinase-like AGPs and AG peptides, were selected for phylogenetic and expression analyses. The expression of these 18 genes was recorded over 48 h following leaf mechanical wounding, as well as in 16 tissue samples representing plants from nature, plants cultivated in vitro, and developmental stages during shoot organogenesis and somatic embryogenesis. None of the selected genes were upregulated during both wounding recovery and regeneration. Possible functions of AGPs with the most interesting expression profiles are discussed.
PB  - Basel: MDPI
T2  - Plants
T1  - The Arabinogalactan Protein Family of Centaurium erythraea Rafn
IS  - 9
VL  - 10
DO  - 10.3390/plants10091870
SP  - 1870
ER  - 

@article{
author = "Paunović, Danijela and Ćuković, Katarina and Bogdanović, Milica and Todorović, Slađana and Trifunović-Momčilov, Milana and Subotić, Angelina and Simonović, Ana and Dragićević, Milan",
year = "2021",
abstract = "Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family of O-glycosylated plant cell surface hydroxyproline-rich glycoproteins (HRGPs). HRGPs/AGPs are intrinsically disordered and not well conserved, making their homology-based mining ineffective. We have applied a recently developed pipeline for HRGP/AGP mining, ragp, which is based on machine learning prediction of proline hydroxylation, to identify HRGP sequences in centaury transcriptome and to classify them into motif and amino acid bias (MAAB) classes. AGP sequences with low AG glycomotif representation were also identified. Six members of each of the three AGP subclasses, fasciclin-like AGPs, receptor kinase-like AGPs and AG peptides, were selected for phylogenetic and expression analyses. The expression of these 18 genes was recorded over 48 h following leaf mechanical wounding, as well as in 16 tissue samples representing plants from nature, plants cultivated in vitro, and developmental stages during shoot organogenesis and somatic embryogenesis. None of the selected genes were upregulated during both wounding recovery and regeneration. Possible functions of AGPs with the most interesting expression profiles are discussed.",
publisher = "Basel: MDPI",
journal = "Plants",
title = "The Arabinogalactan Protein Family of Centaurium erythraea Rafn",
number = "9",
volume = "10",
doi = "10.3390/plants10091870",
pages = "1870"
}

Paunović, D., Ćuković, K., Bogdanović, M., Todorović, S., Trifunović-Momčilov, M., Subotić, A., Simonović, A.,& Dragićević, M.. (2021). The Arabinogalactan Protein Family of Centaurium erythraea Rafn. in Plants
Basel: MDPI., 10(9), 1870.
https://doi.org/10.3390/plants10091870

Paunović D, Ćuković K, Bogdanović M, Todorović S, Trifunović-Momčilov M, Subotić A, Simonović A, Dragićević M. The Arabinogalactan Protein Family of Centaurium erythraea Rafn. in Plants. 2021;10(9):1870.
doi:10.3390/plants10091870 .

Paunović, Danijela, Ćuković, Katarina, Bogdanović, Milica, Todorović, Slađana, Trifunović-Momčilov, Milana, Subotić, Angelina, Simonović, Ana, Dragićević, Milan, "The Arabinogalactan Protein Family of Centaurium erythraea Rafn" in Plants, 10, no. 9 (2021):1870,
https://doi.org/10.3390/plants10091870 . .

TY  - JOUR
AU  - Dragićević, Milan
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Simonović, Ana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3756
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/4966
AB  - Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.
PB  - Oxford University Press
T2  - Glycobiology
T1  - ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R
IS  - 1
IS  - 1
VL  - 30
VL  - 30
DO  - 10.1093/glycob/cwz072
SP  - 19
SP  - 19
EP  - 35
EP  - 35
ER  - 

@article{
author = "Dragićević, Milan and Paunović, Danijela and Bogdanović, Milica and Todorović, Slađana and Simonović, Ana",
year = "2020",
abstract = "Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.",
publisher = "Oxford University Press",
journal = "Glycobiology",
title = "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R",
number = "1, 1",
volume = "30, 30",
doi = "10.1093/glycob/cwz072",
pages = "19-19-35-35"
}

Dragićević, M., Paunović, D., Bogdanović, M., Todorović, S.,& Simonović, A.. (2020). ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology
Oxford University Press., 30(1), 19-35.
https://doi.org/10.1093/glycob/cwz072

Dragićević M, Paunović D, Bogdanović M, Todorović S, Simonović A. ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology. 2020;30(1):19-35.
doi:10.1093/glycob/cwz072 .

Dragićević, Milan, Paunović, Danijela, Bogdanović, Milica, Todorović, Slađana, Simonović, Ana, "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R" in Glycobiology, 30, no. 1 (2020):19-35,
https://doi.org/10.1093/glycob/cwz072 . .

TY  - JOUR
AU  - Dragićević, Milan
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Simonović, Ana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3756
AB  - Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.
PB  - Oxford University Press
T2  - Glycobiology
T1  - ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R
IS  - 1
IS  - 1
VL  - 30
VL  - 30
DO  - 10.1093/glycob/cwz072
SP  - 19
SP  - 19
EP  - 35
EP  - 35
ER  - 

@article{
author = "Dragićević, Milan and Paunović, Danijela and Bogdanović, Milica and Todorović, Slađana and Simonović, Ana",
year = "2020",
abstract = "Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.",
publisher = "Oxford University Press",
journal = "Glycobiology",
title = "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R",
number = "1, 1",
volume = "30, 30",
doi = "10.1093/glycob/cwz072",
pages = "19-19-35-35"
}

Dragićević, M., Paunović, D., Bogdanović, M., Todorović, S.,& Simonović, A.. (2020). ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology
Oxford University Press., 30(1), 19-35.
https://doi.org/10.1093/glycob/cwz072

Dragićević M, Paunović D, Bogdanović M, Todorović S, Simonović A. ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology. 2020;30(1):19-35.
doi:10.1093/glycob/cwz072 .

Dragićević, Milan, Paunović, Danijela, Bogdanović, Milica, Todorović, Slađana, Simonović, Ana, "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R" in Glycobiology, 30, no. 1 (2020):19-35,
https://doi.org/10.1093/glycob/cwz072 . .

TY  - JOUR
AU  - Trifunović-Momčilov, Milana
AU  - Paunović, Danijela
AU  - Milošević, Snežana
AU  - Marković, Marija
AU  - Jevremović, Slađana
AU  - Dragićević, Ivana
AU  - Subotić, Angelina
PY  - 2020
UR  - https://onlinelibrary.wiley.com/doi/abs/10.1111/aab.12593
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3690
AB  - Common centaury (Centaurium erythraea Rafn.) is a plant species that can inhabit saline soils. It is known as a plant with high spontaneous regeneration potential in vitro. In the present work we evaluated shoots and roots salinity tolerance of non-transformed and three AtCKX transgenic centaury lines to graded NaCl concentrations (0, 50, 100, 150, 200 mM) in vitro. Overexpression of AtCKX genes in transgenic centaury plants resulted in an altered cytokinins (CKs) profile leading to a decline of bioactive CK levels and, at the same time, increased contents of storage CK forms, inactive CK forms and/or CK nucleotides. Significant increment of fresh shoot weight was obtained in shoots of non-transformed and AtCKX1 transgenic line only on medium supplemented with 50 mM NaCl. However two analysed AtCKX2 transgenic lines reduced shoot growth at all NaCl concentrations. In general, centaury roots showed higher tolerance to salinity than shoots. Non-transformed and AtCKX1 transgenic lines tolerated up to 100 mM NaCl without change in frequency of regeneration and number of regenerated plants. Roots of two analysed AtCKX2 transgenic lines showed different regeneration potential under salt stress. Regeneration of transgenic AtCKX2-26 shoots even at 200 mM NaCl was recorded. Salinity stress response of centaury shoots and roots was also evaluated at biochemical level. Free proline, malondialdehyde and hydrogen peroxide content as well as antioxidative enzymes activities were investigated in shoots and roots after 1, 2, 4 and 8 weeks. In general, adition of NaCl in culture medium elevated all biochemical parameters in centaury shoots and in roots. Considering that all analysed AtCKX transgenic centaury lines showed altered salt tolerance to graded NaCl concentrations in vitro it can be assumed that CKs might be involved in plant defence to salt stress conditions.
PB  - Blackwell Publishing Ltd
T2  - Annals of Applied Biology
T1  - Salinity stress response of non‐transformed and AtCKX transgenic centaury (Centaurium erythraea Rafn.) shoots and roots grown in vitro
DO  - 10.1111/aab.12593
SP  - aab.12593
ER  - 

@article{
author = "Trifunović-Momčilov, Milana and Paunović, Danijela and Milošević, Snežana and Marković, Marija and Jevremović, Slađana and Dragićević, Ivana and Subotić, Angelina",
year = "2020",
abstract = "Common centaury (Centaurium erythraea Rafn.) is a plant species that can inhabit saline soils. It is known as a plant with high spontaneous regeneration potential in vitro. In the present work we evaluated shoots and roots salinity tolerance of non-transformed and three AtCKX transgenic centaury lines to graded NaCl concentrations (0, 50, 100, 150, 200 mM) in vitro. Overexpression of AtCKX genes in transgenic centaury plants resulted in an altered cytokinins (CKs) profile leading to a decline of bioactive CK levels and, at the same time, increased contents of storage CK forms, inactive CK forms and/or CK nucleotides. Significant increment of fresh shoot weight was obtained in shoots of non-transformed and AtCKX1 transgenic line only on medium supplemented with 50 mM NaCl. However two analysed AtCKX2 transgenic lines reduced shoot growth at all NaCl concentrations. In general, centaury roots showed higher tolerance to salinity than shoots. Non-transformed and AtCKX1 transgenic lines tolerated up to 100 mM NaCl without change in frequency of regeneration and number of regenerated plants. Roots of two analysed AtCKX2 transgenic lines showed different regeneration potential under salt stress. Regeneration of transgenic AtCKX2-26 shoots even at 200 mM NaCl was recorded. Salinity stress response of centaury shoots and roots was also evaluated at biochemical level. Free proline, malondialdehyde and hydrogen peroxide content as well as antioxidative enzymes activities were investigated in shoots and roots after 1, 2, 4 and 8 weeks. In general, adition of NaCl in culture medium elevated all biochemical parameters in centaury shoots and in roots. Considering that all analysed AtCKX transgenic centaury lines showed altered salt tolerance to graded NaCl concentrations in vitro it can be assumed that CKs might be involved in plant defence to salt stress conditions.",
publisher = "Blackwell Publishing Ltd",
journal = "Annals of Applied Biology",
title = "Salinity stress response of non‐transformed and AtCKX transgenic centaury (Centaurium erythraea Rafn.) shoots and roots grown in vitro",
doi = "10.1111/aab.12593",
pages = "aab.12593"
}

Trifunović-Momčilov, M., Paunović, D., Milošević, S., Marković, M., Jevremović, S., Dragićević, I.,& Subotić, A.. (2020). Salinity stress response of non‐transformed and AtCKX transgenic centaury (Centaurium erythraea Rafn.) shoots and roots grown in vitro. in Annals of Applied Biology
Blackwell Publishing Ltd., aab.12593.
https://doi.org/10.1111/aab.12593

Trifunović-Momčilov M, Paunović D, Milošević S, Marković M, Jevremović S, Dragićević I, Subotić A. Salinity stress response of non‐transformed and AtCKX transgenic centaury (Centaurium erythraea Rafn.) shoots and roots grown in vitro. in Annals of Applied Biology. 2020;:aab.12593.
doi:10.1111/aab.12593 .

Trifunović-Momčilov, Milana, Paunović, Danijela, Milošević, Snežana, Marković, Marija, Jevremović, Slađana, Dragićević, Ivana, Subotić, Angelina, "Salinity stress response of non‐transformed and AtCKX transgenic centaury (Centaurium erythraea Rafn.) shoots and roots grown in vitro" in Annals of Applied Biology (2020):aab.12593,
https://doi.org/10.1111/aab.12593 . .

TY  - JOUR
AU  - Ćuković, Katarina
AU  - Dragićević, Milan
AU  - Bogdanović, Milica
AU  - Paunović, Danijela
AU  - Giurato, Giorgio
AU  - Filipović, Biljana
AU  - Subotić, Angelina
AU  - Todorović, Slađana
AU  - Simonović, Ana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3686
AB  - Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites.
PB  - Springer
T2  - Plant Cell, Tissue and Organ Culture
T1  - Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
IS  - 2
VL  - 141
DO  - 10.1007/s11240-020-01801-w
SP  - 417
EP  - 433
ER  - 

@article{
author = "Ćuković, Katarina and Dragićević, Milan and Bogdanović, Milica and Paunović, Danijela and Giurato, Giorgio and Filipović, Biljana and Subotić, Angelina and Todorović, Slađana and Simonović, Ana",
year = "2020",
abstract = "Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites.",
publisher = "Springer",
journal = "Plant Cell, Tissue and Organ Culture",
title = "Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis",
number = "2",
volume = "141",
doi = "10.1007/s11240-020-01801-w",
pages = "417-433"
}

Ćuković, K., Dragićević, M., Bogdanović, M., Paunović, D., Giurato, G., Filipović, B., Subotić, A., Todorović, S.,& Simonović, A.. (2020). Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis. in Plant Cell, Tissue and Organ Culture
Springer., 141(2), 417-433.
https://doi.org/10.1007/s11240-020-01801-w

Ćuković K, Dragićević M, Bogdanović M, Paunović D, Giurato G, Filipović B, Subotić A, Todorović S, Simonović A. Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis. in Plant Cell, Tissue and Organ Culture. 2020;141(2):417-433.
doi:10.1007/s11240-020-01801-w .

Ćuković, Katarina, Dragićević, Milan, Bogdanović, Milica, Paunović, Danijela, Giurato, Giorgio, Filipović, Biljana, Subotić, Angelina, Todorović, Slađana, Simonović, Ana, "Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis" in Plant Cell, Tissue and Organ Culture, 141, no. 2 (2020):417-433,
https://doi.org/10.1007/s11240-020-01801-w . .

TY  - CONF
AU  - Trifunović-Momčilov, Milana
AU  - Motyka, Vaclav
AU  - Dragićević, Ivana
AU  - Paunović, Danijela
AU  - Marković, Marija
AU  - Subotić, Angelina
PY  - 2018
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6322
AB  - Common centaury (Centaurium erythraea Rafn) is a medicinal plant that can inhabit saline soils.
Previous in vitro studies revealed centaury’s tolerance to salinity concerning shoot regeneration
and development. Centaury is known to spontaneously regenerate shoots from root segments
in vitro on hormone-free medium, probably due to endogenous levels of cytokinins (CKs) and
indolyl-3-acetic acid and their balance in roots. In this study we have investigated in vitro shoot
regeneration from root segments, i.e. frequency of shoot regeneration, the average number of regenerated shoots per explant and shoot biomass production in three transformed centaury lines,
bearing AtCKX1 or AtCKX2 genes. Graded concentrations of NaCl (0–200 mM) were added to the
nutrition medium during 8-week cultivation period. As previously shown, selected transformed
centaury lines grown in vitro were characterized by differently reduced bioactive CK contents, as a
consequence of different expression of transgenes. The main goal was to elucidate if changed CK
homeostasis interferes with salt-tolerance and affects shoot regeneration in centaury. The selected AtCKX centaury lines significantly differed from each other in terms of capacity for spontaneous
shoot regeneration and biomass production in vitro. NaCl lowered shoot regeneration in all of
the investigated lines, although they differed in their sensitivity to salt. Both AtCKX2 lines showed
increased sensitivity to NaCl with the highest sensitivity found in one with the highest potential for
spontaneous regeneration (AtCKX2-26). Concentration of 50 mM NaCl enhanced biomass production only in control and line AtCKX1-29. Our results indicate connection between CK homeostasis,
regeneration capacity and tolerance to salinity.
PB  - elgrade: Serbian Plant Physiology Society; Institute for Biological Research "Siniša Stanković"; Faculty of Biology
C3  - Book of abstracts. 3rd International Conference on Plant Biology (22nd SPPS Meeting); 2018 Jun 9-12; Belgrade, Serbia
T1  - Shoot regeneration from root segments in AtCKX transformed centaury lines grown at graded NaCl concentrations in vitro
SP  - 33
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6322
ER  - 

@conference{
author = "Trifunović-Momčilov, Milana and Motyka, Vaclav and Dragićević, Ivana and Paunović, Danijela and Marković, Marija and Subotić, Angelina",
year = "2018",
abstract = "Common centaury (Centaurium erythraea Rafn) is a medicinal plant that can inhabit saline soils.
Previous in vitro studies revealed centaury’s tolerance to salinity concerning shoot regeneration
and development. Centaury is known to spontaneously regenerate shoots from root segments
in vitro on hormone-free medium, probably due to endogenous levels of cytokinins (CKs) and
indolyl-3-acetic acid and their balance in roots. In this study we have investigated in vitro shoot
regeneration from root segments, i.e. frequency of shoot regeneration, the average number of regenerated shoots per explant and shoot biomass production in three transformed centaury lines,
bearing AtCKX1 or AtCKX2 genes. Graded concentrations of NaCl (0–200 mM) were added to the
nutrition medium during 8-week cultivation period. As previously shown, selected transformed
centaury lines grown in vitro were characterized by differently reduced bioactive CK contents, as a
consequence of different expression of transgenes. The main goal was to elucidate if changed CK
homeostasis interferes with salt-tolerance and affects shoot regeneration in centaury. The selected AtCKX centaury lines significantly differed from each other in terms of capacity for spontaneous
shoot regeneration and biomass production in vitro. NaCl lowered shoot regeneration in all of
the investigated lines, although they differed in their sensitivity to salt. Both AtCKX2 lines showed
increased sensitivity to NaCl with the highest sensitivity found in one with the highest potential for
spontaneous regeneration (AtCKX2-26). Concentration of 50 mM NaCl enhanced biomass production only in control and line AtCKX1-29. Our results indicate connection between CK homeostasis,
regeneration capacity and tolerance to salinity.",
publisher = "elgrade: Serbian Plant Physiology Society; Institute for Biological Research "Siniša Stanković"; Faculty of Biology",
journal = "Book of abstracts. 3rd International Conference on Plant Biology (22nd SPPS Meeting); 2018 Jun 9-12; Belgrade, Serbia",
title = "Shoot regeneration from root segments in AtCKX transformed centaury lines grown at graded NaCl concentrations in vitro",
pages = "33",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6322"
}

Trifunović-Momčilov, M., Motyka, V., Dragićević, I., Paunović, D., Marković, M.,& Subotić, A.. (2018). Shoot regeneration from root segments in AtCKX transformed centaury lines grown at graded NaCl concentrations in vitro. in Book of abstracts. 3rd International Conference on Plant Biology (22nd SPPS Meeting); 2018 Jun 9-12; Belgrade, Serbia
elgrade: Serbian Plant Physiology Society; Institute for Biological Research "Siniša Stanković"; Faculty of Biology., 33.
https://hdl.handle.net/21.15107/rcub_ibiss_6322

Trifunović-Momčilov M, Motyka V, Dragićević I, Paunović D, Marković M, Subotić A. Shoot regeneration from root segments in AtCKX transformed centaury lines grown at graded NaCl concentrations in vitro. in Book of abstracts. 3rd International Conference on Plant Biology (22nd SPPS Meeting); 2018 Jun 9-12; Belgrade, Serbia. 2018;:33.
https://hdl.handle.net/21.15107/rcub_ibiss_6322 .

Trifunović-Momčilov, Milana, Motyka, Vaclav, Dragićević, Ivana, Paunović, Danijela, Marković, Marija, Subotić, Angelina, "Shoot regeneration from root segments in AtCKX transformed centaury lines grown at graded NaCl concentrations in vitro" in Book of abstracts. 3rd International Conference on Plant Biology (22nd SPPS Meeting); 2018 Jun 9-12; Belgrade, Serbia (2018):33,
https://hdl.handle.net/21.15107/rcub_ibiss_6322 .

TY  - CONF
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Simonović, Ana
AU  - Dragićević, Milan
PY  - 2018
UR  - https://ojs.pmf.uns.ac.rs/index.php/dbe_serbica/issue/view/25
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4341
AB  - Plant Hydroxyproline rich glycoproteins (HGRPs) comprise a highly diverse family of cell wall macromolecules, involved in a wide array of physiological functions such as cell expansion, somatic embryogenesis, self-incompatibility, signaling and pathogen responses. Due to biased amino acid composition, abundant in disorder promoting residues, HRGPs are intrinsically disordered proteins. The lack of a stable structure lessens the sequence constraints imposed on these proteins and hampers efforts for homology based identification. Current mining approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences.

Herby we present ragp, an R package for HGRP mining with a pipeline which emphasizes finding chimeric and short HRGP’s which is especially useful for identification of arabinogalactan proteins. The ragp pipeline exploits one of HGRP key features, the presence of hydroxyprolines which represent glycosylation sites. These sites are identified using a gradient boosting model trained on plant sequences with experimentally determined hydroxyprolines, based on the local (21-mer) sequence around the target prolines. The model was validated on a set of sequences which were not used during the model building, as well as by using several resampling approaches. Apart from prediction of proline hydroxylation main ragp features include efficient communication with web servers for prediction of N-terminal signal peptides and GPI modification sites, sequence annotation by querying hmmscan, GO enrichment based on predicted pfam domains, and the ability to classify prototypical HRGPs. 

ragp represents the first implementation of a HRGP mining workflow in the R statistical language. It implements common strategies for finding and classifying HRGP sequences along with an optional step where proline hydroxylation is estimated which leads to increased sensitivity and specificity of the filtered sequences. Since R is one of the leading bioinformatics platforms, the filtered sequences can be further analyzed by many specialized packages using the same environment.
PB  - Novi Sad: Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad
C3  - Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89
T1  - ragp: An R toolbox for mining Hydroxyproline rich glycoproteins
SP  - 89
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_4341
ER  - 

@conference{
author = "Paunović, Danijela and Bogdanović, Milica and Todorović, Slađana and Simonović, Ana and Dragićević, Milan",
year = "2018",
abstract = "Plant Hydroxyproline rich glycoproteins (HGRPs) comprise a highly diverse family of cell wall macromolecules, involved in a wide array of physiological functions such as cell expansion, somatic embryogenesis, self-incompatibility, signaling and pathogen responses. Due to biased amino acid composition, abundant in disorder promoting residues, HRGPs are intrinsically disordered proteins. The lack of a stable structure lessens the sequence constraints imposed on these proteins and hampers efforts for homology based identification. Current mining approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences.

Herby we present ragp, an R package for HGRP mining with a pipeline which emphasizes finding chimeric and short HRGP’s which is especially useful for identification of arabinogalactan proteins. The ragp pipeline exploits one of HGRP key features, the presence of hydroxyprolines which represent glycosylation sites. These sites are identified using a gradient boosting model trained on plant sequences with experimentally determined hydroxyprolines, based on the local (21-mer) sequence around the target prolines. The model was validated on a set of sequences which were not used during the model building, as well as by using several resampling approaches. Apart from prediction of proline hydroxylation main ragp features include efficient communication with web servers for prediction of N-terminal signal peptides and GPI modification sites, sequence annotation by querying hmmscan, GO enrichment based on predicted pfam domains, and the ability to classify prototypical HRGPs. 

ragp represents the first implementation of a HRGP mining workflow in the R statistical language. It implements common strategies for finding and classifying HRGP sequences along with an optional step where proline hydroxylation is estimated which leads to increased sensitivity and specificity of the filtered sequences. Since R is one of the leading bioinformatics platforms, the filtered sequences can be further analyzed by many specialized packages using the same environment.",
publisher = "Novi Sad: Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad",
journal = "Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89",
title = "ragp: An R toolbox for mining Hydroxyproline rich glycoproteins",
pages = "89",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_4341"
}

Paunović, D., Bogdanović, M., Todorović, S., Simonović, A.,& Dragićević, M.. (2018). ragp: An R toolbox for mining Hydroxyproline rich glycoproteins. in Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89
Novi Sad: Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad., 89.
https://hdl.handle.net/21.15107/rcub_ibiss_4341

Paunović D, Bogdanović M, Todorović S, Simonović A, Dragićević M. ragp: An R toolbox for mining Hydroxyproline rich glycoproteins. in Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89. 2018;:89.
https://hdl.handle.net/21.15107/rcub_ibiss_4341 .

Paunović, Danijela, Bogdanović, Milica, Todorović, Slađana, Simonović, Ana, Dragićević, Milan, "ragp: An R toolbox for mining Hydroxyproline rich glycoproteins" in Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89 (2018):89,
https://hdl.handle.net/21.15107/rcub_ibiss_4341 .

TY  - CONF
AU  - Simonović, Ana
AU  - Bogdanović, Milica
AU  - Dragićević, Milan
AU  - Ćuković, Katarina
AU  - Subotić, Angelina
AU  - Paunović, Danijela
AU  - Todorović, Slađana
PY  - 2018
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4339
AB  - Kičica je lekovita biljka bogata sekoiridoidima i ksantonima. Potreba za in vitro razmnožavanjem kičice je dovela do razvoja protokola za mikropropagaciju, organogenezu, somatsku embriogenezu (SE), kulturu ćelija, kalusa i korenova i genetičke transformacije.1 Kičica ima izvanredan regeneracioni potencijal i morfogenetsku plastičnost in vitro.1 Polazeći od pretpostavke da se geni uključeni u morfogenezu kod ovakve biljke lako aktiviraju pod induktivnim in vitro uslovima, te da se mogu detektovati kao transkripti potencijalnih markera SE i organogeneze, u cilju identifikacije tih gena smo uspostavili eksperimantalno-analitički sistem koji obuhvata: 1) protokole organogeneze, SE i transformacije; 2) foto-informacioni sistem za "time-laps" dokumentaciju razvoja biljaka in vitro; 3) sekvencirane i rekonstruisane transkriptome lista, korena, embriogenog kalusa, globularnih i kotiledonarnih somatskih embriona i adventivnih pupoljaka kičice; 4) bioinformatičke metode anotacije i analize transkriptoma; 5) identifikovane diferencijalno eksprimirane gene; 6) kolekciju od 17 tkiva/RNK uzoraka za qPCR analizu; 7) set referentnih gena konstantne ekspresije, kao i 8) sofisticiran bioinformatički metod u R-u za identifikaciju proteina sa hidroksiprolinom. Ovaj metod ima primenu u pretrazi biljnih proteina bogatih hidroksiprolinom, a kod kičice će biti korišćen za identifikaciju arabinogalaktanskih proteina, za koje smo pokazali da se indukuju tokom morfogeneze.2,3
PB  - Belgrade: Serbian Biological Society
C3  - Drugi kongres biologa Srbije, Kladovo
T1  - Identifikacija gena koji učestvuju u morfogenezi in vitro kod kičice (Centaurium erythraea Rafn.)
SP  - 44
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_4339
ER  - 

@conference{
author = "Simonović, Ana and Bogdanović, Milica and Dragićević, Milan and Ćuković, Katarina and Subotić, Angelina and Paunović, Danijela and Todorović, Slađana",
year = "2018",
abstract = "Kičica je lekovita biljka bogata sekoiridoidima i ksantonima. Potreba za in vitro razmnožavanjem kičice je dovela do razvoja protokola za mikropropagaciju, organogenezu, somatsku embriogenezu (SE), kulturu ćelija, kalusa i korenova i genetičke transformacije.1 Kičica ima izvanredan regeneracioni potencijal i morfogenetsku plastičnost in vitro.1 Polazeći od pretpostavke da se geni uključeni u morfogenezu kod ovakve biljke lako aktiviraju pod induktivnim in vitro uslovima, te da se mogu detektovati kao transkripti potencijalnih markera SE i organogeneze, u cilju identifikacije tih gena smo uspostavili eksperimantalno-analitički sistem koji obuhvata: 1) protokole organogeneze, SE i transformacije; 2) foto-informacioni sistem za "time-laps" dokumentaciju razvoja biljaka in vitro; 3) sekvencirane i rekonstruisane transkriptome lista, korena, embriogenog kalusa, globularnih i kotiledonarnih somatskih embriona i adventivnih pupoljaka kičice; 4) bioinformatičke metode anotacije i analize transkriptoma; 5) identifikovane diferencijalno eksprimirane gene; 6) kolekciju od 17 tkiva/RNK uzoraka za qPCR analizu; 7) set referentnih gena konstantne ekspresije, kao i 8) sofisticiran bioinformatički metod u R-u za identifikaciju proteina sa hidroksiprolinom. Ovaj metod ima primenu u pretrazi biljnih proteina bogatih hidroksiprolinom, a kod kičice će biti korišćen za identifikaciju arabinogalaktanskih proteina, za koje smo pokazali da se indukuju tokom morfogeneze.2,3",
publisher = "Belgrade: Serbian Biological Society",
journal = "Drugi kongres biologa Srbije, Kladovo",
title = "Identifikacija gena koji učestvuju u morfogenezi in vitro kod kičice (Centaurium erythraea Rafn.)",
pages = "44",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_4339"
}

Simonović, A., Bogdanović, M., Dragićević, M., Ćuković, K., Subotić, A., Paunović, D.,& Todorović, S.. (2018). Identifikacija gena koji učestvuju u morfogenezi in vitro kod kičice (Centaurium erythraea Rafn.). in Drugi kongres biologa Srbije, Kladovo
Belgrade: Serbian Biological Society., 44.
https://hdl.handle.net/21.15107/rcub_ibiss_4339

Simonović A, Bogdanović M, Dragićević M, Ćuković K, Subotić A, Paunović D, Todorović S. Identifikacija gena koji učestvuju u morfogenezi in vitro kod kičice (Centaurium erythraea Rafn.). in Drugi kongres biologa Srbije, Kladovo. 2018;:44.
https://hdl.handle.net/21.15107/rcub_ibiss_4339 .

Simonović, Ana, Bogdanović, Milica, Dragićević, Milan, Ćuković, Katarina, Subotić, Angelina, Paunović, Danijela, Todorović, Slađana, "Identifikacija gena koji učestvuju u morfogenezi in vitro kod kičice (Centaurium erythraea Rafn.)" in Drugi kongres biologa Srbije, Kladovo (2018):44,
https://hdl.handle.net/21.15107/rcub_ibiss_4339 .

TY  - CONF
AU  - Antonić, Dragana
AU  - Milošević, Snežana
AU  - Dragićević, Milan
AU  - Simonović, Ana
AU  - Paunović, Danijela
AU  - Momčilović, Ivana
AU  - Subotić, Angelina
PY  - 2018
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4338
AB  - Impatiens walleriana is an important ornamental plant with a tendency to quickly wilt when
exposed to dehydration, which considerably affects its commercial value. However, Impatiens also
has great potential to rehydrate upon watering. Effective protection of this valuable ornamental
from water stress requires understanding the events associated with dehydration and rehydration
at the molecular level. Dehydrins (DHNs) are highly hydrophilic proteins whose expression in many
plant species has been correlated with several types of abiotic stresses, including drought, salinity,
and cold. Dehydrins comprise Group II of late embryogenesis abundant (LEA) proteins, known to
be associated with plant responses to water deficit. DHNs lack stable tridimensional structures, so
they are considered intrinsically disordered proteins. They are characterized by three conserved
sequence motifs marked as a K (Lys-rich), Y (Tyr-rich) and S (Ser-rich). To study the expression of
Dhn genes in response to drought, we have sequenced I. walleriana transcriptome and identified
IwDhn transcripts from RNA-seq data using HMMER (hmmscan, v3.1b2) and Pfam 31 database.
Quantitative RT-PCR revealed that two IwDhn genes are extremely upregulated in drought, while
one has constitutive expression. It can be speculated that fast rehydration after drought stress is at
least in part result of the protective role of dehydrins.
PB  - Belgrade: Serbian Plant Physiology Society
C3  - 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade
T1  - Expression of dehydrins in Impatiens walleriana exposed to drought
SP  - 74
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_4338
ER  - 

@conference{
author = "Antonić, Dragana and Milošević, Snežana and Dragićević, Milan and Simonović, Ana and Paunović, Danijela and Momčilović, Ivana and Subotić, Angelina",
year = "2018",
abstract = "Impatiens walleriana is an important ornamental plant with a tendency to quickly wilt when
exposed to dehydration, which considerably affects its commercial value. However, Impatiens also
has great potential to rehydrate upon watering. Effective protection of this valuable ornamental
from water stress requires understanding the events associated with dehydration and rehydration
at the molecular level. Dehydrins (DHNs) are highly hydrophilic proteins whose expression in many
plant species has been correlated with several types of abiotic stresses, including drought, salinity,
and cold. Dehydrins comprise Group II of late embryogenesis abundant (LEA) proteins, known to
be associated with plant responses to water deficit. DHNs lack stable tridimensional structures, so
they are considered intrinsically disordered proteins. They are characterized by three conserved
sequence motifs marked as a K (Lys-rich), Y (Tyr-rich) and S (Ser-rich). To study the expression of
Dhn genes in response to drought, we have sequenced I. walleriana transcriptome and identified
IwDhn transcripts from RNA-seq data using HMMER (hmmscan, v3.1b2) and Pfam 31 database.
Quantitative RT-PCR revealed that two IwDhn genes are extremely upregulated in drought, while
one has constitutive expression. It can be speculated that fast rehydration after drought stress is at
least in part result of the protective role of dehydrins.",
publisher = "Belgrade: Serbian Plant Physiology Society",
journal = "3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade",
title = "Expression of dehydrins in Impatiens walleriana exposed to drought",
pages = "74",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_4338"
}

Antonić, D., Milošević, S., Dragićević, M., Simonović, A., Paunović, D., Momčilović, I.,& Subotić, A.. (2018). Expression of dehydrins in Impatiens walleriana exposed to drought. in 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade
Belgrade: Serbian Plant Physiology Society., 74.
https://hdl.handle.net/21.15107/rcub_ibiss_4338

Antonić D, Milošević S, Dragićević M, Simonović A, Paunović D, Momčilović I, Subotić A. Expression of dehydrins in Impatiens walleriana exposed to drought. in 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade. 2018;:74.
https://hdl.handle.net/21.15107/rcub_ibiss_4338 .

Antonić, Dragana, Milošević, Snežana, Dragićević, Milan, Simonović, Ana, Paunović, Danijela, Momčilović, Ivana, Subotić, Angelina, "Expression of dehydrins in Impatiens walleriana exposed to drought" in 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade (2018):74,
https://hdl.handle.net/21.15107/rcub_ibiss_4338 .

TY  - CONF
AU  - Ćuković, Katarina
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Dragićević, Milan
AU  - Todorović, Slađana
AU  - Subotić, Angelina
AU  - Simonović, Ana
PY  - 2018
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4335
AB  - Centaurium erythraea Rafn (Gentianaceae) is a medicinal plant, rich in secondary metabolites,
mainly secoiridoid glucosides and xanthones, known for numerous beneficial effects on human
health. In addition, C. erythraea possesses remarkable developmental plasticity and is easily cultured
in vitro, so it represents a suitable model system for studying developmental biology. One
of the most notable illustrations of plant cell totipotency is the capability of certain somatic plant
cells to initiate embryogenic development through somatic embryogenesis (SE). It has been proposed
that mechanical wounding during in vitro manipulations of plant material can promote cell
differentiation and somatic embryo development. Our recent research is based on elucidating
the gene expression profiles of centaury tissues in response to wounding and in different SE stages
using quantitative real-time PCR. Considering the fact that these processes exhibit a dynamic
genetic activity, the selection of stable reference genes is paramount in order to obtain unbiased
conclusions. Hereby we report selection of stable reference genes in C. erythraea for studying gene
expression during somatic embryogenesis and wounding. Thirteen frequently used reference
genes were selected and their expression stability was assessed in different developmental stages,
including globular and cotyledonary stages of embryos, as well as wounded tissues. Specific sets
of primers were designed relying on previously obtained next-generation RNA sequencing data.
The results were interpreted using two algorithmic approaches - geNorm and NormFinder - and
the most stable reference genes from a set of tested candidate genes were determined.
PB  - Belgrade: Serbian Plant Physiology Society
C3  - 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade
T1  - Selection of stable reference genes in Centaurium erythraea Rafn during in vitro somatic embryogenesis and mechanical wounding
SP  - 28
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_4335
ER  - 

@conference{
author = "Ćuković, Katarina and Paunović, Danijela and Bogdanović, Milica and Dragićević, Milan and Todorović, Slađana and Subotić, Angelina and Simonović, Ana",
year = "2018",
abstract = "Centaurium erythraea Rafn (Gentianaceae) is a medicinal plant, rich in secondary metabolites,
mainly secoiridoid glucosides and xanthones, known for numerous beneficial effects on human
health. In addition, C. erythraea possesses remarkable developmental plasticity and is easily cultured
in vitro, so it represents a suitable model system for studying developmental biology. One
of the most notable illustrations of plant cell totipotency is the capability of certain somatic plant
cells to initiate embryogenic development through somatic embryogenesis (SE). It has been proposed
that mechanical wounding during in vitro manipulations of plant material can promote cell
differentiation and somatic embryo development. Our recent research is based on elucidating
the gene expression profiles of centaury tissues in response to wounding and in different SE stages
using quantitative real-time PCR. Considering the fact that these processes exhibit a dynamic
genetic activity, the selection of stable reference genes is paramount in order to obtain unbiased
conclusions. Hereby we report selection of stable reference genes in C. erythraea for studying gene
expression during somatic embryogenesis and wounding. Thirteen frequently used reference
genes were selected and their expression stability was assessed in different developmental stages,
including globular and cotyledonary stages of embryos, as well as wounded tissues. Specific sets
of primers were designed relying on previously obtained next-generation RNA sequencing data.
The results were interpreted using two algorithmic approaches - geNorm and NormFinder - and
the most stable reference genes from a set of tested candidate genes were determined.",
publisher = "Belgrade: Serbian Plant Physiology Society",
journal = "3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade",
title = "Selection of stable reference genes in Centaurium erythraea Rafn during in vitro somatic embryogenesis and mechanical wounding",
pages = "28",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_4335"
}

Ćuković, K., Paunović, D., Bogdanović, M., Dragićević, M., Todorović, S., Subotić, A.,& Simonović, A.. (2018). Selection of stable reference genes in Centaurium erythraea Rafn during in vitro somatic embryogenesis and mechanical wounding. in 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade
Belgrade: Serbian Plant Physiology Society., 28.
https://hdl.handle.net/21.15107/rcub_ibiss_4335

Ćuković K, Paunović D, Bogdanović M, Dragićević M, Todorović S, Subotić A, Simonović A. Selection of stable reference genes in Centaurium erythraea Rafn during in vitro somatic embryogenesis and mechanical wounding. in 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade. 2018;:28.
https://hdl.handle.net/21.15107/rcub_ibiss_4335 .

Ćuković, Katarina, Paunović, Danijela, Bogdanović, Milica, Dragićević, Milan, Todorović, Slađana, Subotić, Angelina, Simonović, Ana, "Selection of stable reference genes in Centaurium erythraea Rafn during in vitro somatic embryogenesis and mechanical wounding" in 3rd International Conference on Plant Biology (22nd SPPS Meeting), Belgrade (2018):28,
https://hdl.handle.net/21.15107/rcub_ibiss_4335 .

TY  - CONF
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Trifunović-Momčilov, Milana
AU  - Todorović, Slađana
AU  - Simonović, Ana
AU  - Subotić, Angelina
AU  - Dragićević, Milan
PY  - 2018
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4342
AB  - Arabinogalactan proteins (AGPs) are cell wall proteoglycans with important roles during plant
growth and development. They comprise one of the most complex families of macromolecules
found in plants, which is in part due to the incredible diversity of the glycans decorating the pro-
tein backbone, as well as the heterogeneity of the protein backbones. While this diversity is cer-
tainly responsible for the wide array of physiological functions associated with AGPs, it hampers
efforts for homology-based identification. We have developed a new method for filtering AGP se-
quences that exploits one of their key features, the presence of hydroxyprolines, which represent
glycosylation sites. This method was used to filter potential AGPs from Centaurium erythraea RNA-
seq data. Most of the filtered sequences had no identifiable domains, while the most frequent
identified domains were the Protein kinase and Protein tyrosine kinase domains identified in the
same sequences, followed by well-known AGP associates, Leucine rich repeats, Probable lipid
transfer, Plastocyanin-like and Fasciclin. It is noteworthy that the Protein (tyrosine) kinase domain
has thus far eluded experimental evidence for linkage with AGPs in any plant species, probably
due to its transmembrane nature. The implicated sequences were examined in depth and com-
pared to homologs from Arabidopsis.
PB  - Belgrade: Serbian Plant Physiology Society
C3  - Book of Abstracts, 3rd International Conference on Plant biology, 9.-12. June 2018., Belgrade, Serbia
T1  - Are receptor tyrosine kinases chimeric AGP’s?
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_4342
ER  - 

@conference{
author = "Paunović, Danijela and Bogdanović, Milica and Trifunović-Momčilov, Milana and Todorović, Slađana and Simonović, Ana and Subotić, Angelina and Dragićević, Milan",
year = "2018",
abstract = "Arabinogalactan proteins (AGPs) are cell wall proteoglycans with important roles during plant
growth and development. They comprise one of the most complex families of macromolecules
found in plants, which is in part due to the incredible diversity of the glycans decorating the pro-
tein backbone, as well as the heterogeneity of the protein backbones. While this diversity is cer-
tainly responsible for the wide array of physiological functions associated with AGPs, it hampers
efforts for homology-based identification. We have developed a new method for filtering AGP se-
quences that exploits one of their key features, the presence of hydroxyprolines, which represent
glycosylation sites. This method was used to filter potential AGPs from Centaurium erythraea RNA-
seq data. Most of the filtered sequences had no identifiable domains, while the most frequent
identified domains were the Protein kinase and Protein tyrosine kinase domains identified in the
same sequences, followed by well-known AGP associates, Leucine rich repeats, Probable lipid
transfer, Plastocyanin-like and Fasciclin. It is noteworthy that the Protein (tyrosine) kinase domain
has thus far eluded experimental evidence for linkage with AGPs in any plant species, probably
due to its transmembrane nature. The implicated sequences were examined in depth and com-
pared to homologs from Arabidopsis.",
publisher = "Belgrade: Serbian Plant Physiology Society",
journal = "Book of Abstracts, 3rd International Conference on Plant biology, 9.-12. June 2018., Belgrade, Serbia",
title = "Are receptor tyrosine kinases chimeric AGP’s?",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_4342"
}

Paunović, D., Bogdanović, M., Trifunović-Momčilov, M., Todorović, S., Simonović, A., Subotić, A.,& Dragićević, M.. (2018). Are receptor tyrosine kinases chimeric AGP’s?. in Book of Abstracts, 3rd International Conference on Plant biology, 9.-12. June 2018., Belgrade, Serbia
Belgrade: Serbian Plant Physiology Society..
https://hdl.handle.net/21.15107/rcub_ibiss_4342

Paunović D, Bogdanović M, Trifunović-Momčilov M, Todorović S, Simonović A, Subotić A, Dragićević M. Are receptor tyrosine kinases chimeric AGP’s?. in Book of Abstracts, 3rd International Conference on Plant biology, 9.-12. June 2018., Belgrade, Serbia. 2018;.
https://hdl.handle.net/21.15107/rcub_ibiss_4342 .

Paunović, Danijela, Bogdanović, Milica, Trifunović-Momčilov, Milana, Todorović, Slađana, Simonović, Ana, Subotić, Angelina, Dragićević, Milan, "Are receptor tyrosine kinases chimeric AGP’s?" in Book of Abstracts, 3rd International Conference on Plant biology, 9.-12. June 2018., Belgrade, Serbia (2018),
https://hdl.handle.net/21.15107/rcub_ibiss_4342 .

TY  - JOUR
AU  - Trifunović-Momčilov, Milana
AU  - Tadić, Vojin
AU  - Petrić, Marija
AU  - Paunović, Danijela
AU  - Jevremović, Slađana
AU  - Subotić, Angelina
PY  - 2014
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/2222
AB  - Arabinogalactan proteins (AGPs) are a family of highly glycosylated cell
   surface proteins located at the plasma membrane and plant cell wall.
   AGPs play important roles in plant growth and development. Yariv
   phenylglycoside (beta GlcY), synthetic red-brown dye that specifically
   binds and precipitates AGPs, has been used for detection and
   quantification of AGPs in plant tissue. Graded concentrations of beta
   GlcY (0-75 mu M) were used to investigate the effect of this synthetic
   dye on induction of in vitro morphogenesis in Centaurium erythraea root
   culture on two nutrient media: A1/2MS and A1/2MS + IBA 1.0 mu M.
   Regeneration of C. erythraea shoots on root explants was stimulated on
   both media supplemented with 25 mu M beta GlcY after 8 weeks in culture.
   Quantification of AGPs in different tissues of C. erythraea was
   determinate with single radial diffusion method. This work emphasizes
   clear effect of beta GlcY on induction of morphogenesis in vitro in C.
   erythraea root culture.
T2  - Acta Physiologiae Plantarum
T1  - Quantification of arabinogalactan proteins during in vitro morphogenesis
 induced by beta-D-glucosyl Yariv reagent in Centaurium erythraea root
 culture
IS  - 5
VL  - 36
DO  - 10.1007/s11738-014-1495-y
SP  - 1187
EP  - 1195
ER  - 

@article{
author = "Trifunović-Momčilov, Milana and Tadić, Vojin and Petrić, Marija and Paunović, Danijela and Jevremović, Slađana and Subotić, Angelina",
year = "2014",
abstract = "Arabinogalactan proteins (AGPs) are a family of highly glycosylated cell
   surface proteins located at the plasma membrane and plant cell wall.
   AGPs play important roles in plant growth and development. Yariv
   phenylglycoside (beta GlcY), synthetic red-brown dye that specifically
   binds and precipitates AGPs, has been used for detection and
   quantification of AGPs in plant tissue. Graded concentrations of beta
   GlcY (0-75 mu M) were used to investigate the effect of this synthetic
   dye on induction of in vitro morphogenesis in Centaurium erythraea root
   culture on two nutrient media: A1/2MS and A1/2MS + IBA 1.0 mu M.
   Regeneration of C. erythraea shoots on root explants was stimulated on
   both media supplemented with 25 mu M beta GlcY after 8 weeks in culture.
   Quantification of AGPs in different tissues of C. erythraea was
   determinate with single radial diffusion method. This work emphasizes
   clear effect of beta GlcY on induction of morphogenesis in vitro in C.
   erythraea root culture.",
journal = "Acta Physiologiae Plantarum",
title = "Quantification of arabinogalactan proteins during in vitro morphogenesis
 induced by beta-D-glucosyl Yariv reagent in Centaurium erythraea root
 culture",
number = "5",
volume = "36",
doi = "10.1007/s11738-014-1495-y",
pages = "1187-1195"
}

Trifunović-Momčilov, M., Tadić, V., Petrić, M., Paunović, D., Jevremović, S.,& Subotić, A.. (2014). Quantification of arabinogalactan proteins during in vitro morphogenesis
 induced by beta-D-glucosyl Yariv reagent in Centaurium erythraea root
 culture. in Acta Physiologiae Plantarum, 36(5), 1187-1195.
https://doi.org/10.1007/s11738-014-1495-y

Trifunović-Momčilov M, Tadić V, Petrić M, Paunović D, Jevremović S, Subotić A. Quantification of arabinogalactan proteins during in vitro morphogenesis
 induced by beta-D-glucosyl Yariv reagent in Centaurium erythraea root
 culture. in Acta Physiologiae Plantarum. 2014;36(5):1187-1195.
doi:10.1007/s11738-014-1495-y .

Trifunović-Momčilov, Milana, Tadić, Vojin, Petrić, Marija, Paunović, Danijela, Jevremović, Slađana, Subotić, Angelina, "Quantification of arabinogalactan proteins during in vitro morphogenesis
 induced by beta-D-glucosyl Yariv reagent in Centaurium erythraea root
 culture" in Acta Physiologiae Plantarum, 36, no. 5 (2014):1187-1195,
https://doi.org/10.1007/s11738-014-1495-y . .