TY  - JOUR
AU  - Nikolić, Dragana
AU  - Bosnić, Dragana
AU  - Samardžić, Jelena
PY  - 2023
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2023.1039053
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1884
UR  - https://doi.org/10.3389/fpls.2023.1039053
AB  - Essential micronutrients belonging to the transition metals, such as Fe and Cu, are indispensable for plant growth and stress tolerance; however, when present in excess, they can become potentially dangerous producers of reactive oxygen species. Therefore, their homeostases must be strictly regulated. Both microelement deficiencies and elevated concentrations of heavy metals in the soil are global problems that reduce the nutritional value of crops and seriously affect human health. Silicon, a beneficial element known for its protective properties, has been reported to alleviate the symptoms of Cu toxicity and Fe deficiency stress in plants; however, we are still far from a comprehensive understanding of the underlying molecular mechanisms. Although Si-mediated mitigation of these stresses has been clearly demonstrated for some species, the effects of Si vary depending on plant species, growing conditions and experimental design. In this review, the proposed mechanistic models explaining the effect of Si are summarized and discussed. Iron and copper compete for the common metal transporters and share the same transport routes, hence, inadequate concentration of one element leads to disturbances of another. Silicon is reported to beneficially influence not only the distribution of the element supplied below or above the optimal concentration, but also the distribution of other microelements, as well as their molar ratios. The influence of Si on Cu immobilization and retention in the root, as well as Si-induced Fe remobilization from the source to the sink organs are of vital importance. The changes in cellular Cu and Fe localization are considered to play a crucial role in restoring homeostasis of these microelements. Silicon has been shown to stimulate the accumulation of metal chelators involved in both the mobilization of deficient elements and scavenging excess heavy metals. Research into the mechanisms of the ameliorative effects of Si is valuable for reducing mineral stress in plants and improving the nutritional value of crops. This review aims to provide a thorough and critical overview of the current state of knowledge in this field and to discuss discrepancies in the observed effects of Si and different views on its mode of action.
T2  - Frontiers in Plant Science
T2  - Frontiers in Plant Science
T1  - Silicon in action: Between iron scarcity and excess copper
VL  - 14
DO  - doi.org/10.3389/fpls.2023.1039053
ER  - 

@article{
author = "Nikolić, Dragana and Bosnić, Dragana and Samardžić, Jelena",
year = "2023",
abstract = "Essential micronutrients belonging to the transition metals, such as Fe and Cu, are indispensable for plant growth and stress tolerance; however, when present in excess, they can become potentially dangerous producers of reactive oxygen species. Therefore, their homeostases must be strictly regulated. Both microelement deficiencies and elevated concentrations of heavy metals in the soil are global problems that reduce the nutritional value of crops and seriously affect human health. Silicon, a beneficial element known for its protective properties, has been reported to alleviate the symptoms of Cu toxicity and Fe deficiency stress in plants; however, we are still far from a comprehensive understanding of the underlying molecular mechanisms. Although Si-mediated mitigation of these stresses has been clearly demonstrated for some species, the effects of Si vary depending on plant species, growing conditions and experimental design. In this review, the proposed mechanistic models explaining the effect of Si are summarized and discussed. Iron and copper compete for the common metal transporters and share the same transport routes, hence, inadequate concentration of one element leads to disturbances of another. Silicon is reported to beneficially influence not only the distribution of the element supplied below or above the optimal concentration, but also the distribution of other microelements, as well as their molar ratios. The influence of Si on Cu immobilization and retention in the root, as well as Si-induced Fe remobilization from the source to the sink organs are of vital importance. The changes in cellular Cu and Fe localization are considered to play a crucial role in restoring homeostasis of these microelements. Silicon has been shown to stimulate the accumulation of metal chelators involved in both the mobilization of deficient elements and scavenging excess heavy metals. Research into the mechanisms of the ameliorative effects of Si is valuable for reducing mineral stress in plants and improving the nutritional value of crops. This review aims to provide a thorough and critical overview of the current state of knowledge in this field and to discuss discrepancies in the observed effects of Si and different views on its mode of action.",
journal = "Frontiers in Plant Science, Frontiers in Plant Science",
title = "Silicon in action: Between iron scarcity and excess copper",
volume = "14",
doi = "doi.org/10.3389/fpls.2023.1039053"
}

Nikolić, D., Bosnić, D.,& Samardžić, J.. (2023). Silicon in action: Between iron scarcity and excess copper. in Frontiers in Plant Science, 14.
https://doi.org/doi.org/10.3389/fpls.2023.1039053

Nikolić D, Bosnić D, Samardžić J. Silicon in action: Between iron scarcity and excess copper. in Frontiers in Plant Science. 2023;14.
doi:doi.org/10.3389/fpls.2023.1039053 .

Nikolić, Dragana, Bosnić, Dragana, Samardžić, Jelena, "Silicon in action: Between iron scarcity and excess copper" in Frontiers in Plant Science, 14 (2023),
https://doi.org/doi.org/10.3389/fpls.2023.1039053 . .

TY  - CONF
AU  - Nikolić, Dragana
AU  - Divac Rankov, Aleksandra
AU  - Samardžić, Jelena
AU  - Pantelić, Ana
AU  - Spasovski, Vesna
AU  - Banović Đeri, Bojana
AU  - Kosanović, Maja
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2266
AB  - Outer membrane vesicles (OMVs), extracellular vesicles (EVs) produced by Gram-negative bacteria, are
increasingly recognised as promising tools in biomedicine due to their innate ability to interact with human
cells and trigger immune responses. The interaction of OMVs of plant growth-promoting bacteria (PGPB) with
plants, as well as with plant-pathogenic microorganisms, is far less explored. Considering the great
importance of PGPBs for the development of sustainable, environmentally friendly solutions in agriculture, the
study of the role of OMVs in PGPB-plant and PGPB-phytopathogen interactions holds valuable application
potential.
To investigate PGPB OMVs, we isolated and characterised OMVs produced by Paraburkholderia phytofirmans
PsJN, a PGPB strain known to enhance plant resistance to various abiotic and biotic stresses. After testing
different methods for isolating and purifying OMVs, a commercially available affinity-based column system
was selected as the most efficient. Outer membrane origin of isolated OMVs was confirmed using an essay for
detection of lipopolysaccharide (LPS).
To examine the interaction of OMVs with plant cells, Arabidopsis thaliana roots were incubated with isolated
P. phytofirmans PsJN vesicles, previously labelled with lipid binding fluorescent dye Vybrant™ DiD. Red signals
were observed, under confocal laser scanning microscope, in root hairs and root surface in DiD-OMV treated
plants, while in control-treated roots the same signals were missing. The results suggest direct contact of
OMVs with root hairs, which are necessary for nutrient acquisition and plant-microbe interactions in
rhizosphere. Our further research is focused on the characterization of OMV-associated RNA and its potential
delivery into host plant cells.
PB  - Serbian Society for Extracellular Vesicles (SrbEVs)
PB  - Austrian Society for Extracellular Vesicles (ASEV)
PB  - Hungarian Society for Extracellular Vesicles (HSEV)
PB  - Slovenian Network for Extracellular Vesicles (SiN-EV)
C3  - Small New World 2.0
T1  - Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots
EP  - 109
SP  - 109
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2266
ER  - 

@conference{
author = "Nikolić, Dragana and Divac Rankov, Aleksandra and Samardžić, Jelena and Pantelić, Ana and Spasovski, Vesna and Banović Đeri, Bojana and Kosanović, Maja",
year = "2023",
abstract = "Outer membrane vesicles (OMVs), extracellular vesicles (EVs) produced by Gram-negative bacteria, are
increasingly recognised as promising tools in biomedicine due to their innate ability to interact with human
cells and trigger immune responses. The interaction of OMVs of plant growth-promoting bacteria (PGPB) with
plants, as well as with plant-pathogenic microorganisms, is far less explored. Considering the great
importance of PGPBs for the development of sustainable, environmentally friendly solutions in agriculture, the
study of the role of OMVs in PGPB-plant and PGPB-phytopathogen interactions holds valuable application
potential.
To investigate PGPB OMVs, we isolated and characterised OMVs produced by Paraburkholderia phytofirmans
PsJN, a PGPB strain known to enhance plant resistance to various abiotic and biotic stresses. After testing
different methods for isolating and purifying OMVs, a commercially available affinity-based column system
was selected as the most efficient. Outer membrane origin of isolated OMVs was confirmed using an essay for
detection of lipopolysaccharide (LPS).
To examine the interaction of OMVs with plant cells, Arabidopsis thaliana roots were incubated with isolated
P. phytofirmans PsJN vesicles, previously labelled with lipid binding fluorescent dye Vybrant™ DiD. Red signals
were observed, under confocal laser scanning microscope, in root hairs and root surface in DiD-OMV treated
plants, while in control-treated roots the same signals were missing. The results suggest direct contact of
OMVs with root hairs, which are necessary for nutrient acquisition and plant-microbe interactions in
rhizosphere. Our further research is focused on the characterization of OMV-associated RNA and its potential
delivery into host plant cells.",
publisher = "Serbian Society for Extracellular Vesicles (SrbEVs), Austrian Society for Extracellular Vesicles (ASEV), Hungarian Society for Extracellular Vesicles (HSEV), Slovenian Network for Extracellular Vesicles (SiN-EV)",
journal = "Small New World 2.0",
title = "Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots",
pages = "109-109",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2266"
}

Nikolić, D., Divac Rankov, A., Samardžić, J., Pantelić, A., Spasovski, V., Banović Đeri, B.,& Kosanović, M.. (2023). Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots. in Small New World 2.0
Serbian Society for Extracellular Vesicles (SrbEVs)., 109-109.
https://hdl.handle.net/21.15107/rcub_imagine_2266

Nikolić D, Divac Rankov A, Samardžić J, Pantelić A, Spasovski V, Banović Đeri B, Kosanović M. Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots. in Small New World 2.0. 2023;:109-109.
https://hdl.handle.net/21.15107/rcub_imagine_2266 .

Nikolić, Dragana, Divac Rankov, Aleksandra, Samardžić, Jelena, Pantelić, Ana, Spasovski, Vesna, Banović Đeri, Bojana, Kosanović, Maja, "Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots" in Small New World 2.0 (2023):109-109,
https://hdl.handle.net/21.15107/rcub_imagine_2266 .

TY  - JOUR
AU  - Nikolić, Ivana
AU  - Samardžić, Jelena
AU  - Stevanović, Strahinja
AU  - Miljuš-Đukić, Jovanka
AU  - Milisavljević, Mira
AU  - Timotijević, Gordana
PY  - 2023
UR  - https://www.mdpi.com/1422-0067/24/3/2442
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1883
AB  - Global climate change has a detrimental effect on plant growth and health, causing serious losses in agriculture. Investigation of the molecular mechanisms of plant responses to various environmental pressures and the generation of plants tolerant to abiotic stress are imperative to modern plant science. In this paper, we focus on the application of the well-established technology CRISPR/Cas9 genome editing to better understand the functioning of the intrinsically disordered protein DSS1 in plant response to oxidative stress. The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were phenotypically characterized during plant development and their sensitivity to oxidative stress was analyzed. The characterization of mutant lines revealed differences in root and stem lengths, and rosette area size. Plants with a disrupted AtDSS1(V) gene exhibited lower survival rates and increased levels of oxidized proteins in comparison to WT plants exposed to oxidative stress induced by hydrogen peroxide. In this work, the dss1 double mutant was not obtained due to embryonic lethality. These results suggest that the DSS1(V) protein could be an important molecular component in plant abiotic stress response
T2  - International Journal of Molecular Sciences
T2  - International Journal of Molecular Sciences
T1  - CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response
IS  - 3
SP  - 2442
VL  - 24
DO  - 10.3390/ijms24032442
ER  - 

@article{
author = "Nikolić, Ivana and Samardžić, Jelena and Stevanović, Strahinja and Miljuš-Đukić, Jovanka and Milisavljević, Mira and Timotijević, Gordana",
year = "2023",
abstract = "Global climate change has a detrimental effect on plant growth and health, causing serious losses in agriculture. Investigation of the molecular mechanisms of plant responses to various environmental pressures and the generation of plants tolerant to abiotic stress are imperative to modern plant science. In this paper, we focus on the application of the well-established technology CRISPR/Cas9 genome editing to better understand the functioning of the intrinsically disordered protein DSS1 in plant response to oxidative stress. The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were phenotypically characterized during plant development and their sensitivity to oxidative stress was analyzed. The characterization of mutant lines revealed differences in root and stem lengths, and rosette area size. Plants with a disrupted AtDSS1(V) gene exhibited lower survival rates and increased levels of oxidized proteins in comparison to WT plants exposed to oxidative stress induced by hydrogen peroxide. In this work, the dss1 double mutant was not obtained due to embryonic lethality. These results suggest that the DSS1(V) protein could be an important molecular component in plant abiotic stress response",
journal = "International Journal of Molecular Sciences, International Journal of Molecular Sciences",
title = "CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response",
number = "3",
pages = "2442",
volume = "24",
doi = "10.3390/ijms24032442"
}

Nikolić, I., Samardžić, J., Stevanović, S., Miljuš-Đukić, J., Milisavljević, M.,& Timotijević, G.. (2023). CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response. in International Journal of Molecular Sciences, 24(3), 2442.
https://doi.org/10.3390/ijms24032442

Nikolić I, Samardžić J, Stevanović S, Miljuš-Đukić J, Milisavljević M, Timotijević G. CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response. in International Journal of Molecular Sciences. 2023;24(3):2442.
doi:10.3390/ijms24032442 .

Nikolić, Ivana, Samardžić, Jelena, Stevanović, Strahinja, Miljuš-Đukić, Jovanka, Milisavljević, Mira, Timotijević, Gordana, "CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response" in International Journal of Molecular Sciences, 24, no. 3 (2023):2442,
https://doi.org/10.3390/ijms24032442 . .

TY  - JOUR
AU  - Petrović, Gordana
AU  - Živanović, Tomislav
AU  - Nikolić, Zorica
AU  - Vasiljević, Sanja
AU  - Milošević, Dragana
AU  - Stanisavljević, Nemanja
AU  - Samardžić, Jelena
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2148
AB  - Background: This study was carried out for an understanding of the antioxidant mechanisms of field pea varieties under osmotic stress conditions caused by a lack of water. The activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APx) and glutathione reductase (GR) were examined and analyzed. The gene expression levels of Cu/Zn SOD, cAPx and GR genes were also examined. Methods: Osmotic stress was stimulated using PEG 6000 with the osmotic potential of -0.1 MPa in 10 days old plant seedlings. The activity of the antioxidant enzymes was measured in the shoots and roots of pea seedlings. The gene expression levels of genes coding antioxidative enzymes were examined by the reverse transcription polymerase chain reaction (RT-PCR) technique. Arabidopsis 18S rRNA was used as endogenous control. Result: Osmotic stress changed the activities of antioxidant enzymes in the shoots and roots of pea seedlings. Varieties more tolerant to osmotic stress showed a significant increase in antioxidant activities in shoots and roots, while sensitive varieties showed a significant decrease. The results of the analysis of the expression of genes, coding for antioxidant enzymes, showed that the reaction of the tested cultivars to ROS was the result of increased expression of the tested genes in tolerant cultivars, i.e. decreased expression in sensitive cultivars.
PB  - Agricultural Research Communication Centre
T2  - Legume Research
T2  - Legume Research
T1  - Drought-induced Changes in the Antioxidant System in Pisum sativum L.
DO  - 10.18805/LRF-755
ER  - 

@article{
author = "Petrović, Gordana and Živanović, Tomislav and Nikolić, Zorica and Vasiljević, Sanja and Milošević, Dragana and Stanisavljević, Nemanja and Samardžić, Jelena",
year = "2023",
abstract = "Background: This study was carried out for an understanding of the antioxidant mechanisms of field pea varieties under osmotic stress conditions caused by a lack of water. The activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APx) and glutathione reductase (GR) were examined and analyzed. The gene expression levels of Cu/Zn SOD, cAPx and GR genes were also examined. Methods: Osmotic stress was stimulated using PEG 6000 with the osmotic potential of -0.1 MPa in 10 days old plant seedlings. The activity of the antioxidant enzymes was measured in the shoots and roots of pea seedlings. The gene expression levels of genes coding antioxidative enzymes were examined by the reverse transcription polymerase chain reaction (RT-PCR) technique. Arabidopsis 18S rRNA was used as endogenous control. Result: Osmotic stress changed the activities of antioxidant enzymes in the shoots and roots of pea seedlings. Varieties more tolerant to osmotic stress showed a significant increase in antioxidant activities in shoots and roots, while sensitive varieties showed a significant decrease. The results of the analysis of the expression of genes, coding for antioxidant enzymes, showed that the reaction of the tested cultivars to ROS was the result of increased expression of the tested genes in tolerant cultivars, i.e. decreased expression in sensitive cultivars.",
publisher = "Agricultural Research Communication Centre",
journal = "Legume Research, Legume Research",
title = "Drought-induced Changes in the Antioxidant System in Pisum sativum L.",
doi = "10.18805/LRF-755"
}

Petrović, G., Živanović, T., Nikolić, Z., Vasiljević, S., Milošević, D., Stanisavljević, N.,& Samardžić, J.. (2023). Drought-induced Changes in the Antioxidant System in Pisum sativum L.. in Legume Research
Agricultural Research Communication Centre..
https://doi.org/10.18805/LRF-755

Petrović G, Živanović T, Nikolić Z, Vasiljević S, Milošević D, Stanisavljević N, Samardžić J. Drought-induced Changes in the Antioxidant System in Pisum sativum L.. in Legume Research. 2023;.
doi:10.18805/LRF-755 .

Petrović, Gordana, Živanović, Tomislav, Nikolić, Zorica, Vasiljević, Sanja, Milošević, Dragana, Stanisavljević, Nemanja, Samardžić, Jelena, "Drought-induced Changes in the Antioxidant System in Pisum sativum L." in Legume Research (2023),
https://doi.org/10.18805/LRF-755 . .

TY  - CONF
AU  - Demir, Arnela
AU  - Selović, Alisa
AU  - Dahija, Sabina
AU  - Parić, Adisa
AU  - Samardžić, Jelena
AU  - Karalija, Erna
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1906
AB  - To improve our understanding of the molecular mechanisms underlying seed priming, RNA
transcriptome analysis was performed using primed and non-primed seeds of Silene sendtneri. Seed
priming was performed by submerging the seeds in different priming agents for 24h at 4°C, followed
by rinsing with sterilized water and desiccation to the original moisture content. Silene sendtneri is a
species with no sequenced genome and annotation of de novo assembly of the transcriptome was done
using different species for the reference genome. Gene ontology (GO) analysis indicated that genes
related to heavy metal transporters and heat shock proteins are differentially expressed after priming in
relation to the used priming agent. Within these gene categories, genes such as heavy metal-associated
isoprenylated plant protein 26-like (log2fold -8.79) were downregulated, while others such as heavy
metal ATPase 5 (log2fold 6.46), heat shock factor protein HSF30-like isoform X1 (log2fold 5,98) were
upregulated. Some gene categories are commonly highly expressed after seed priming regardless of the
used agent, but some specific gene categories have been recorded to be expressed in relation to the used
agent.
PB  - Sarajevo : Institute for Genetic Engineering and Biotechnology, University of Sarajevo
C3  - Genetics & Applications
T1  - Seed priming enhances tolerance and accumulation of heavy metals in cd hyperaccumulator silene sendtneri through changes in gene expression
IS  - 2 (Special edition)
SP  - 143
VL  - 7
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1906
ER  - 

@conference{
author = "Demir, Arnela and Selović, Alisa and Dahija, Sabina and Parić, Adisa and Samardžić, Jelena and Karalija, Erna",
year = "2023",
abstract = "To improve our understanding of the molecular mechanisms underlying seed priming, RNA
transcriptome analysis was performed using primed and non-primed seeds of Silene sendtneri. Seed
priming was performed by submerging the seeds in different priming agents for 24h at 4°C, followed
by rinsing with sterilized water and desiccation to the original moisture content. Silene sendtneri is a
species with no sequenced genome and annotation of de novo assembly of the transcriptome was done
using different species for the reference genome. Gene ontology (GO) analysis indicated that genes
related to heavy metal transporters and heat shock proteins are differentially expressed after priming in
relation to the used priming agent. Within these gene categories, genes such as heavy metal-associated
isoprenylated plant protein 26-like (log2fold -8.79) were downregulated, while others such as heavy
metal ATPase 5 (log2fold 6.46), heat shock factor protein HSF30-like isoform X1 (log2fold 5,98) were
upregulated. Some gene categories are commonly highly expressed after seed priming regardless of the
used agent, but some specific gene categories have been recorded to be expressed in relation to the used
agent.",
publisher = "Sarajevo : Institute for Genetic Engineering and Biotechnology, University of Sarajevo",
journal = "Genetics & Applications",
title = "Seed priming enhances tolerance and accumulation of heavy metals in cd hyperaccumulator silene sendtneri through changes in gene expression",
number = "2 (Special edition)",
pages = "143",
volume = "7",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1906"
}

Demir, A., Selović, A., Dahija, S., Parić, A., Samardžić, J.,& Karalija, E.. (2023). Seed priming enhances tolerance and accumulation of heavy metals in cd hyperaccumulator silene sendtneri through changes in gene expression. in Genetics & Applications
Sarajevo : Institute for Genetic Engineering and Biotechnology, University of Sarajevo., 7(2 (Special edition)), 143.
https://hdl.handle.net/21.15107/rcub_imagine_1906

Demir A, Selović A, Dahija S, Parić A, Samardžić J, Karalija E. Seed priming enhances tolerance and accumulation of heavy metals in cd hyperaccumulator silene sendtneri through changes in gene expression. in Genetics & Applications. 2023;7(2 (Special edition)):143.
https://hdl.handle.net/21.15107/rcub_imagine_1906 .

Demir, Arnela, Selović, Alisa, Dahija, Sabina, Parić, Adisa, Samardžić, Jelena, Karalija, Erna, "Seed priming enhances tolerance and accumulation of heavy metals in cd hyperaccumulator silene sendtneri through changes in gene expression" in Genetics & Applications, 7, no. 2 (Special edition) (2023):143,
https://hdl.handle.net/21.15107/rcub_imagine_1906 .

TY  - CONF
AU  - Nešić, Sofija
AU  - Pantelić, Ana
AU  - Samardžić, Jelena
AU  - Nikolić, Dragana
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2158
AB  - Plant growth promoting bacteria (PGPB) are microorganisms present in plant
rhizosphere that stimulate plant growth, as well as prime plants against abiotic
and biotic stress. PGPB are also located in plant intercellular space and can directly
interfere with plant pathogens. Many different mechanisms of interaction
between plants and PGPB has been shown, but the interaction through outer
membrane vesicles (OMVs) has only been proposed. OMVs are membrane-enclosed
nanostructures produced by Gram-negative bacteria. Size of OMVs can
range from 20 to 300 nm, depending on the strain. In this research, we determined
optimal method for isolation of OMVs produced by Paraburkholderia
phytofirmans PsJN, characterized the size range of OMVs, their concentration
and origin. OMVs from PGPB PsJN have been isolated us\ing two methodological
approaches: 1) differential centrifugation, ultrafiltration, and purification
using Optiprep density gradient, and 2) OMV isolation by the commercial
ExoBacteria OMV Isolation Kit that uses an affinity-based column system. Size
and concentration of isolated OMVs were analyzed using Nanoparticle Tracking
Analysis (NTA). As the OMVs are derived from outer membranes of bacteria, their
origin has been proven using an essay for detection of lipopolysaccharides. In
addition, protein profiles of OMV from PsJN were visualized by SDS-PAGE. Comparing
different methods for isolation and purification of vesicles from PsJN we
concluded that for our PGPB strain the commercial ExoBacteria OMV Isolation
Kit provides the highest yield. Quantification of OMV using NTA of OMVs produced
by P. phytofirmans PsJN, isolated with the commercial kit, showed a mean
particle numeration of 4.05*109 particles/ml. Size of OMVs isolated from PsJN
ranged from 50 to 200 nm. Detection of lipopolysaccharides confirmed that
isolated vesicles originated from outer membranes of PsJN. These findings are
the important first step in our research of the role of OMVs in PGPB interaction
with plants.
PB  - Belgrade : Faculty of Biology
C3  - ICGEB WORKSHOP: Trends in microbial solutions for sustainable agriculture
T1  - Characterization of outer membrane vesicles of plant growth promoting bacteria Paraburkholderia phytofirmans PsJN
EP  - 72
SP  - 72
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2158
ER  - 

@conference{
author = "Nešić, Sofija and Pantelić, Ana and Samardžić, Jelena and Nikolić, Dragana",
year = "2023",
abstract = "Plant growth promoting bacteria (PGPB) are microorganisms present in plant
rhizosphere that stimulate plant growth, as well as prime plants against abiotic
and biotic stress. PGPB are also located in plant intercellular space and can directly
interfere with plant pathogens. Many different mechanisms of interaction
between plants and PGPB has been shown, but the interaction through outer
membrane vesicles (OMVs) has only been proposed. OMVs are membrane-enclosed
nanostructures produced by Gram-negative bacteria. Size of OMVs can
range from 20 to 300 nm, depending on the strain. In this research, we determined
optimal method for isolation of OMVs produced by Paraburkholderia
phytofirmans PsJN, characterized the size range of OMVs, their concentration
and origin. OMVs from PGPB PsJN have been isolated us\ing two methodological
approaches: 1) differential centrifugation, ultrafiltration, and purification
using Optiprep density gradient, and 2) OMV isolation by the commercial
ExoBacteria OMV Isolation Kit that uses an affinity-based column system. Size
and concentration of isolated OMVs were analyzed using Nanoparticle Tracking
Analysis (NTA). As the OMVs are derived from outer membranes of bacteria, their
origin has been proven using an essay for detection of lipopolysaccharides. In
addition, protein profiles of OMV from PsJN were visualized by SDS-PAGE. Comparing
different methods for isolation and purification of vesicles from PsJN we
concluded that for our PGPB strain the commercial ExoBacteria OMV Isolation
Kit provides the highest yield. Quantification of OMV using NTA of OMVs produced
by P. phytofirmans PsJN, isolated with the commercial kit, showed a mean
particle numeration of 4.05*109 particles/ml. Size of OMVs isolated from PsJN
ranged from 50 to 200 nm. Detection of lipopolysaccharides confirmed that
isolated vesicles originated from outer membranes of PsJN. These findings are
the important first step in our research of the role of OMVs in PGPB interaction
with plants.",
publisher = "Belgrade : Faculty of Biology",
journal = "ICGEB WORKSHOP: Trends in microbial solutions for sustainable agriculture",
title = "Characterization of outer membrane vesicles of plant growth promoting bacteria Paraburkholderia phytofirmans PsJN",
pages = "72-72",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2158"
}

Nešić, S., Pantelić, A., Samardžić, J.,& Nikolić, D.. (2023). Characterization of outer membrane vesicles of plant growth promoting bacteria Paraburkholderia phytofirmans PsJN. in ICGEB WORKSHOP: Trends in microbial solutions for sustainable agriculture
Belgrade : Faculty of Biology., 72-72.
https://hdl.handle.net/21.15107/rcub_imagine_2158

Nešić S, Pantelić A, Samardžić J, Nikolić D. Characterization of outer membrane vesicles of plant growth promoting bacteria Paraburkholderia phytofirmans PsJN. in ICGEB WORKSHOP: Trends in microbial solutions for sustainable agriculture. 2023;:72-72.
https://hdl.handle.net/21.15107/rcub_imagine_2158 .

Nešić, Sofija, Pantelić, Ana, Samardžić, Jelena, Nikolić, Dragana, "Characterization of outer membrane vesicles of plant growth promoting bacteria Paraburkholderia phytofirmans PsJN" in ICGEB WORKSHOP: Trends in microbial solutions for sustainable agriculture (2023):72-72,
https://hdl.handle.net/21.15107/rcub_imagine_2158 .

TY  - CONF
AU  - Milić, Dejana
AU  - Pantelić, Ana
AU  - Samardžić, Jelena
AU  - Banović Đeri, Bojana
AU  - Vidović, Marija
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2035
AB  - Variegated Pelargonium zonale is a widely cultivated ornamental plant characterized by
green, photosynthetically active tissue (GL) and white, non-photosynthetic tissue (WL).
The aim of this study was to investigate the transcriptomic differences between these
two tissue types.
We performed RNA-seq analysis of GL and WL on Illumina HiSeq 2500 platform. The
raw reads were processed using in-house scripts to remove low-quality reads, adapter
sequences, poly-N sequences, and contaminants. High-quality clean reads were subjected
to de novo transcriptome assembly using Trinity (min_kmer_cov = 2, min_glue = 2). The
redundancy was removed and longest transcripts per cluster were selected as unigenes.
Gene expression levels were estimated using RSEM by mapping clean data back to the
assembled transcriptome (Bowtie2 with mismatch = 0). Differential expression analysis
between GL and WL (three biological replicates per each) was performed with DESeq2
R package (p values adjusted according to Benjamini and Hochberg for controlling False
Discovery Rate). Genes with abs (log2 FC) ≥ 2 and adjusted p value < 0.05 were assigned
as statistically significant differentially expressed. Functional enrichment analysis was
performed using GOseq R package and KOBAS software (corrected p < 0.05).
We annotated 85,374 unigenes (61.17%), providing a valuable resource for future
functional genomics studies. Out of 8896 gene clusters that were statistically significantly
differentially expressed between the green and white leaf tissues (p value < 0.05 and
abs(log2 fold change) ≥ 2), 5585 were upregulated in the WL, while 3311 were upregulated
in the GL. These findings shed light on the transcriptomic differences between the
two leaf tissue types in P. zonale and provide a foundation for further research on the
functional significance of these differences. Also, this study demonstrated utility of the
Trinity pipeline for de novo transcriptomic analysis of organism whose genomes are yet
not sequenced.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale
EP  - 90
SP  - 90
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2035
ER  - 

@conference{
author = "Milić, Dejana and Pantelić, Ana and Samardžić, Jelena and Banović Đeri, Bojana and Vidović, Marija",
year = "2023",
abstract = "Variegated Pelargonium zonale is a widely cultivated ornamental plant characterized by
green, photosynthetically active tissue (GL) and white, non-photosynthetic tissue (WL).
The aim of this study was to investigate the transcriptomic differences between these
two tissue types.
We performed RNA-seq analysis of GL and WL on Illumina HiSeq 2500 platform. The
raw reads were processed using in-house scripts to remove low-quality reads, adapter
sequences, poly-N sequences, and contaminants. High-quality clean reads were subjected
to de novo transcriptome assembly using Trinity (min_kmer_cov = 2, min_glue = 2). The
redundancy was removed and longest transcripts per cluster were selected as unigenes.
Gene expression levels were estimated using RSEM by mapping clean data back to the
assembled transcriptome (Bowtie2 with mismatch = 0). Differential expression analysis
between GL and WL (three biological replicates per each) was performed with DESeq2
R package (p values adjusted according to Benjamini and Hochberg for controlling False
Discovery Rate). Genes with abs (log2 FC) ≥ 2 and adjusted p value < 0.05 were assigned
as statistically significant differentially expressed. Functional enrichment analysis was
performed using GOseq R package and KOBAS software (corrected p < 0.05).
We annotated 85,374 unigenes (61.17%), providing a valuable resource for future
functional genomics studies. Out of 8896 gene clusters that were statistically significantly
differentially expressed between the green and white leaf tissues (p value < 0.05 and
abs(log2 fold change) ≥ 2), 5585 were upregulated in the WL, while 3311 were upregulated
in the GL. These findings shed light on the transcriptomic differences between the
two leaf tissue types in P. zonale and provide a foundation for further research on the
functional significance of these differences. Also, this study demonstrated utility of the
Trinity pipeline for de novo transcriptomic analysis of organism whose genomes are yet
not sequenced.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale",
pages = "90-90",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2035"
}

Milić, D., Pantelić, A., Samardžić, J., Banović Đeri, B.,& Vidović, M.. (2023). Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 90-90.
https://hdl.handle.net/21.15107/rcub_imagine_2035

Milić D, Pantelić A, Samardžić J, Banović Đeri B, Vidović M. Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale. in 4th Belgrade Bioinformatics Conference. 2023;4:90-90.
https://hdl.handle.net/21.15107/rcub_imagine_2035 .

Milić, Dejana, Pantelić, Ana, Samardžić, Jelena, Banović Đeri, Bojana, Vidović, Marija, "Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale" in 4th Belgrade Bioinformatics Conference, 4 (2023):90-90,
https://hdl.handle.net/21.15107/rcub_imagine_2035 .

TY  - JOUR
AU  - Petrović, Gordana
AU  - Živanović, Tomislav
AU  - Nikolić, Zorica
AU  - Vasiljević, Sanja
AU  - Milošević, Dragana
AU  - Stanisavljević, Nemanja
AU  - Samardžić, Jelena
PY  - 2023
UR  - https://arccjournals.com/journal/legume-research-an-international-journal/LRF-755
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2166
AB  - Background: This study was carried out for an understanding of the antioxidant mechanisms of field pea varieties under osmotic
stress conditions caused by a lack of water. The activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase
(CAT), ascorbate peroxidase (APx) and glutathione reductase (GR) were examined and analyzed. The gene expression levels of
Cu/Zn SOD, cAPx and GR genes were also examined.
Methods: Osmotic stress was stimulated using PEG 6000 with the osmotic potential of -0.1 MPa in 10 days old plant seedlings. The
activity of the antioxidant enzymes was measured in the shoots and roots of pea seedlings. The gene expression levels of genes
coding antioxidative enzymes were examined by the reverse transcription polymerase chain reaction (RT-PCR) technique. Arabidopsis
18S rRNA was used as endogenous control.
Result: Osmotic stress changed the activities of antioxidant enzymes in the shoots and roots of pea seedlings. Varieties more
tolerant to osmotic stress showed a significant increase in antioxidant activities in shoots and roots, while sensitive varieties showed
a significant decrease. The results of the analysis of the expression of genes, coding for antioxidant enzymes, showed that the
reaction of the tested cultivars to ROS was the result of increased expression of the tested genes in tolerant cultivars, i.e. decreased
expression in sensitive cultivars.
T2  - Legume Research
T1  - Drought-induced Changes in the Antioxidant System in Pisum sativum L.
EP  - 1452
IS  - 11
SP  - 1445
VL  - 46
DO  - 10.18805/LRF-755
ER  - 

@article{
author = "Petrović, Gordana and Živanović, Tomislav and Nikolić, Zorica and Vasiljević, Sanja and Milošević, Dragana and Stanisavljević, Nemanja and Samardžić, Jelena",
year = "2023",
abstract = "Background: This study was carried out for an understanding of the antioxidant mechanisms of field pea varieties under osmotic
stress conditions caused by a lack of water. The activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase
(CAT), ascorbate peroxidase (APx) and glutathione reductase (GR) were examined and analyzed. The gene expression levels of
Cu/Zn SOD, cAPx and GR genes were also examined.
Methods: Osmotic stress was stimulated using PEG 6000 with the osmotic potential of -0.1 MPa in 10 days old plant seedlings. The
activity of the antioxidant enzymes was measured in the shoots and roots of pea seedlings. The gene expression levels of genes
coding antioxidative enzymes were examined by the reverse transcription polymerase chain reaction (RT-PCR) technique. Arabidopsis
18S rRNA was used as endogenous control.
Result: Osmotic stress changed the activities of antioxidant enzymes in the shoots and roots of pea seedlings. Varieties more
tolerant to osmotic stress showed a significant increase in antioxidant activities in shoots and roots, while sensitive varieties showed
a significant decrease. The results of the analysis of the expression of genes, coding for antioxidant enzymes, showed that the
reaction of the tested cultivars to ROS was the result of increased expression of the tested genes in tolerant cultivars, i.e. decreased
expression in sensitive cultivars.",
journal = "Legume Research",
title = "Drought-induced Changes in the Antioxidant System in Pisum sativum L.",
pages = "1452-1445",
number = "11",
volume = "46",
doi = "10.18805/LRF-755"
}

Petrović, G., Živanović, T., Nikolić, Z., Vasiljević, S., Milošević, D., Stanisavljević, N.,& Samardžić, J.. (2023). Drought-induced Changes in the Antioxidant System in Pisum sativum L.. in Legume Research, 46(11), 1445-1452.
https://doi.org/10.18805/LRF-755

Petrović G, Živanović T, Nikolić Z, Vasiljević S, Milošević D, Stanisavljević N, Samardžić J. Drought-induced Changes in the Antioxidant System in Pisum sativum L.. in Legume Research. 2023;46(11):1445-1452.
doi:10.18805/LRF-755 .

Petrović, Gordana, Živanović, Tomislav, Nikolić, Zorica, Vasiljević, Sanja, Milošević, Dragana, Stanisavljević, Nemanja, Samardžić, Jelena, "Drought-induced Changes in the Antioxidant System in Pisum sativum L." in Legume Research, 46, no. 11 (2023):1445-1452,
https://doi.org/10.18805/LRF-755 . .

TY  - JOUR
AU  - Milić, Dejana
AU  - Živanović, Bojana
AU  - Samardžić, Jelena
AU  - Nikolić, Nenad
AU  - Cukier, Caroline
AU  - Limami, Anis M.
AU  - Vidović, Marija
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1712
AB  - Plants are inevitably exposed to extreme climatic conditions that lead to a disturbed balance between the amount of absorbed energy and their ability to process it. Variegated leaves with photosynthetically active green leaf tissue (GL) and photosynthetically inactive white leaf tissue (WL) are an excellent model system to study source–sink interactions within the same leaf under the same microenvironmental conditions. We demonstrated that under excess excitation energy (EEE) conditions (high irradiance and lower temperature), regulated metabolic reprogramming in both leaf tissues allowed an increased consumption of reducing equivalents, as evidenced by preserved maximum efficiency of photosystem II (ФPSII) at the end of the experiment. GL of the EEE-treated plants employed two strategies: (i) the accumulation of flavonoid glycosides, especially cyanidin glycosides, as an alternative electron sink, and (ii) cell wall stiffening by cellulose, pectin, and lignin accumulation. On the other hand, WL increased the amount of free amino acids, mainly arginine, asparagine, branched-chain and aromatic amino acids, as well as kaempferol and quercetin glycosides. Thus, WL acts as an important energy escape valve that is required in order to maintain the successful performance of the GL sectors under EEE conditions. Finally, this role could be an adaptive value of variegation, as no consistent conclusions about its ecological benefits have been proposed so far.
T2  - International Journal of Molecular Sciences
T2  - International Journal of Molecular Sciences
T1  - Carbon and Nitrogen Allocation between the Sink and Source Leaf Tissue in Response to the Excess Excitation Energy Conditions
IS  - 3
SP  - 2269
VL  - 24
DO  - 10.3390/ijms24032269
ER  - 

@article{
author = "Milić, Dejana and Živanović, Bojana and Samardžić, Jelena and Nikolić, Nenad and Cukier, Caroline and Limami, Anis M. and Vidović, Marija",
year = "2023",
abstract = "Plants are inevitably exposed to extreme climatic conditions that lead to a disturbed balance between the amount of absorbed energy and their ability to process it. Variegated leaves with photosynthetically active green leaf tissue (GL) and photosynthetically inactive white leaf tissue (WL) are an excellent model system to study source–sink interactions within the same leaf under the same microenvironmental conditions. We demonstrated that under excess excitation energy (EEE) conditions (high irradiance and lower temperature), regulated metabolic reprogramming in both leaf tissues allowed an increased consumption of reducing equivalents, as evidenced by preserved maximum efficiency of photosystem II (ФPSII) at the end of the experiment. GL of the EEE-treated plants employed two strategies: (i) the accumulation of flavonoid glycosides, especially cyanidin glycosides, as an alternative electron sink, and (ii) cell wall stiffening by cellulose, pectin, and lignin accumulation. On the other hand, WL increased the amount of free amino acids, mainly arginine, asparagine, branched-chain and aromatic amino acids, as well as kaempferol and quercetin glycosides. Thus, WL acts as an important energy escape valve that is required in order to maintain the successful performance of the GL sectors under EEE conditions. Finally, this role could be an adaptive value of variegation, as no consistent conclusions about its ecological benefits have been proposed so far.",
journal = "International Journal of Molecular Sciences, International Journal of Molecular Sciences",
title = "Carbon and Nitrogen Allocation between the Sink and Source Leaf Tissue in Response to the Excess Excitation Energy Conditions",
number = "3",
pages = "2269",
volume = "24",
doi = "10.3390/ijms24032269"
}

Milić, D., Živanović, B., Samardžić, J., Nikolić, N., Cukier, C., Limami, A. M.,& Vidović, M.. (2023). Carbon and Nitrogen Allocation between the Sink and Source Leaf Tissue in Response to the Excess Excitation Energy Conditions. in International Journal of Molecular Sciences, 24(3), 2269.
https://doi.org/10.3390/ijms24032269

Milić D, Živanović B, Samardžić J, Nikolić N, Cukier C, Limami AM, Vidović M. Carbon and Nitrogen Allocation between the Sink and Source Leaf Tissue in Response to the Excess Excitation Energy Conditions. in International Journal of Molecular Sciences. 2023;24(3):2269.
doi:10.3390/ijms24032269 .

Milić, Dejana, Živanović, Bojana, Samardžić, Jelena, Nikolić, Nenad, Cukier, Caroline, Limami, Anis M., Vidović, Marija, "Carbon and Nitrogen Allocation between the Sink and Source Leaf Tissue in Response to the Excess Excitation Energy Conditions" in International Journal of Molecular Sciences, 24, no. 3 (2023):2269,
https://doi.org/10.3390/ijms24032269 . .

TY  - CONF
AU  - Nikolić, Ivana
AU  - Timotijević, Gordana
AU  - Samardžić, Jelena
AU  - Milisavljević, Mira
PY  - 2023
UR  - https://europlantbiology2023.org/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1972
AB  - DSS1 (deletion of split hand/split foot 1) is a highly conserved, eukaryotic, and multifunctional
protein. DSS1 as a small intrinsically disordered protein binds to multiple proteins when it
gains a final conformation. There are two highly homologous genes, DSS1(I) and DSS1(V) in the
Arabidopsis genome. Our aim is to examine Atdss1 mutants through oxidative stress. We
obtained separate stable lines of Arabidopsis containing mutations in DSS1s using
CRISPR/Cas9 technology. After H2O2 treatment, mutant seedlings showed increased
sensitivity to oxidative stress in comparison to WT plants. Transcriptome analysis showed
that dss1(I)del25 and dss1(V)ins18 mutations caused 2762 and 2335 differentially expressed
genes compared to WT under oxidative stress, respectively. We found that upregulated
expression was in genes involved in homologue recombination and RNA transport in both dss1
lines. The most downregulated genes are classified into flavonoid biosynthesis and MAPK
signaling pathway.
PB  - Plant Biology Europe
C3  - 14th International Conference of the French Society of Plant Biology
T1  - Transcriptome analysis of Atdss1 mutants in response to oxidative stress
EP  - 172
SP  - 172
VL  - 14
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1972
ER  - 

@conference{
author = "Nikolić, Ivana and Timotijević, Gordana and Samardžić, Jelena and Milisavljević, Mira",
year = "2023",
abstract = "DSS1 (deletion of split hand/split foot 1) is a highly conserved, eukaryotic, and multifunctional
protein. DSS1 as a small intrinsically disordered protein binds to multiple proteins when it
gains a final conformation. There are two highly homologous genes, DSS1(I) and DSS1(V) in the
Arabidopsis genome. Our aim is to examine Atdss1 mutants through oxidative stress. We
obtained separate stable lines of Arabidopsis containing mutations in DSS1s using
CRISPR/Cas9 technology. After H2O2 treatment, mutant seedlings showed increased
sensitivity to oxidative stress in comparison to WT plants. Transcriptome analysis showed
that dss1(I)del25 and dss1(V)ins18 mutations caused 2762 and 2335 differentially expressed
genes compared to WT under oxidative stress, respectively. We found that upregulated
expression was in genes involved in homologue recombination and RNA transport in both dss1
lines. The most downregulated genes are classified into flavonoid biosynthesis and MAPK
signaling pathway.",
publisher = "Plant Biology Europe",
journal = "14th International Conference of the French Society of Plant Biology",
title = "Transcriptome analysis of Atdss1 mutants in response to oxidative stress",
pages = "172-172",
volume = "14",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1972"
}

Nikolić, I., Timotijević, G., Samardžić, J.,& Milisavljević, M.. (2023). Transcriptome analysis of Atdss1 mutants in response to oxidative stress. in 14th International Conference of the French Society of Plant Biology
Plant Biology Europe., 14, 172-172.
https://hdl.handle.net/21.15107/rcub_imagine_1972

Nikolić I, Timotijević G, Samardžić J, Milisavljević M. Transcriptome analysis of Atdss1 mutants in response to oxidative stress. in 14th International Conference of the French Society of Plant Biology. 2023;14:172-172.
https://hdl.handle.net/21.15107/rcub_imagine_1972 .

Nikolić, Ivana, Timotijević, Gordana, Samardžić, Jelena, Milisavljević, Mira, "Transcriptome analysis of Atdss1 mutants in response to oxidative stress" in 14th International Conference of the French Society of Plant Biology, 14 (2023):172-172,
https://hdl.handle.net/21.15107/rcub_imagine_1972 .

TY  - JOUR
AU  - Milić, Dejana
AU  - Pantelić, Ana
AU  - Banović Đeri, Bojana
AU  - Samardžić, Jelena
AU  - Vidović, Marija
PY  - 2023
UR  - https://www.mdpi.com/1422-0067/24/6/5288
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1795
AB  - The photosynthetically active green leaf (GL) and non-active white leaf (WL) tissues of variegated Pelargonium zonale provide an excellent model system for studying processes associated with photosynthesis and sink-source interactions, enabling the same microenvironmental conditions. By combining differential transcriptomics and metabolomics, we identified the main differences between these two metabolically contrasting tissues. Genes related to photosynthesis and associated pigments, the Calvin–Benson cycle, fermentation, and glycolysis were strongly repressed in WL. On the other hand, genes related to nitrogen and protein metabolism, defence, cytoskeletal components (motor proteins), cell division, DNA replication, repair and recombination, chromatin remodelling, and histone modifications were upregulated in WL. A content of soluble sugars, TCA intermediates, ascorbate, and hydroxybenzoic acids was lower, while the concentration of free amino acids (AAs), hydroxycinnamic acids, and several quercetin and kaempferol glycosides was higher in WL than in GL. Therefore, WL presents a carbon sink and depends on photosynthetic and energy-generating processes in GL. Furthermore, the upregulated nitrogen metabolism in WL compensates for the insufficient energy from carbon metabolism by providing alternative respiratory substrates. At the same time, WL serves as nitrogen storage. Overall, our study provides a new genetic data resource for the use of this excellent model system and for ornamental pelargonium breeding and contributes to uncovering molecular mechanisms underlying variegation and its adaptive ecological value.
T2  - International Journal of Molecular Sciences
T2  - International Journal of Molecular Sciences
T1  - Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study
IS  - 6
SP  - 5288
VL  - 24
DO  - 10.3390/ijms24065288
ER  - 

@article{
author = "Milić, Dejana and Pantelić, Ana and Banović Đeri, Bojana and Samardžić, Jelena and Vidović, Marija",
year = "2023",
abstract = "The photosynthetically active green leaf (GL) and non-active white leaf (WL) tissues of variegated Pelargonium zonale provide an excellent model system for studying processes associated with photosynthesis and sink-source interactions, enabling the same microenvironmental conditions. By combining differential transcriptomics and metabolomics, we identified the main differences between these two metabolically contrasting tissues. Genes related to photosynthesis and associated pigments, the Calvin–Benson cycle, fermentation, and glycolysis were strongly repressed in WL. On the other hand, genes related to nitrogen and protein metabolism, defence, cytoskeletal components (motor proteins), cell division, DNA replication, repair and recombination, chromatin remodelling, and histone modifications were upregulated in WL. A content of soluble sugars, TCA intermediates, ascorbate, and hydroxybenzoic acids was lower, while the concentration of free amino acids (AAs), hydroxycinnamic acids, and several quercetin and kaempferol glycosides was higher in WL than in GL. Therefore, WL presents a carbon sink and depends on photosynthetic and energy-generating processes in GL. Furthermore, the upregulated nitrogen metabolism in WL compensates for the insufficient energy from carbon metabolism by providing alternative respiratory substrates. At the same time, WL serves as nitrogen storage. Overall, our study provides a new genetic data resource for the use of this excellent model system and for ornamental pelargonium breeding and contributes to uncovering molecular mechanisms underlying variegation and its adaptive ecological value.",
journal = "International Journal of Molecular Sciences, International Journal of Molecular Sciences",
title = "Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study",
number = "6",
pages = "5288",
volume = "24",
doi = "10.3390/ijms24065288"
}

Milić, D., Pantelić, A., Banović Đeri, B., Samardžić, J.,& Vidović, M.. (2023). Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study. in International Journal of Molecular Sciences, 24(6), 5288.
https://doi.org/10.3390/ijms24065288

Milić D, Pantelić A, Banović Đeri B, Samardžić J, Vidović M. Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study. in International Journal of Molecular Sciences. 2023;24(6):5288.
doi:10.3390/ijms24065288 .

Milić, Dejana, Pantelić, Ana, Banović Đeri, Bojana, Samardžić, Jelena, Vidović, Marija, "Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study" in International Journal of Molecular Sciences, 24, no. 6 (2023):5288,
https://doi.org/10.3390/ijms24065288 . .

TY  - CONF
AU  - Banović Đeri, Bojana
AU  - Nešić, Sofija
AU  - Pantelić, Ana
AU  - Samardžić, Jelena
AU  - Nikolić, Dragana
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2030
AB  - Bacterial small RNAs (sRNAs) represent a highly diverse RNA class ranging from 8 to 200
nucleotides in length, originating from the bacterial chromosome, plasmids or phages.
After syntheses sRNAs can remain inside the bacterial cell, be secreted or packed into
outer membrane vesicles (OMV), enabling various intra- and inter-kingdom interactions.
Different sRNAs biotypes display differences in structure, mechanism of action and level
of regulation (i.e. transcription, translation, mRNA stability, etc.), but could be broadly
grouped in: trans-acting sRNAs (bind to target mRNAs) and cis-encoded sRNAs (or
antisense RNA that may interact not only with mRNAs, but also with proteins and DNA).
Even though the advancement of high-throughput sequencing technology led to a burst
of knowledge on small RNAs complexity and diversity, there are still specific challenges
related to sRNA-seq data analysis that need to be resolved. Two main challenges,
associated to short length of many bacterial sRNA biotypes, are: (i) to discriminate
between functional sRNAs synthesized by bacterial cell and degradation fragments
produced by sample preparation and (ii) to detect functional sRNAs displaying sequence
variation. While loss of very small sized sRNAs could easily be overcome by cutting-off
only the specific adapter sequences that were used in sRNA library preparation, providing
a proper mapping still remains a strenuous task.
The aim of this study was to test five different mapping tools that are widely used in NGS
data analysis (bbmap, bowtie2, bwa, minimap2 and segemehl) for their performances in
mapping of bacterial OMV sRNA-seq data to bacterial reference genome. For this test
publicly available NCBI sRNA-seq dataset from OMVs of Aliivibrio fischeri (PRJNA629425)
was used, as it contained sRNAs of different length and biotype and because A.fischeri
reference genome and annotation were available (PRJNA12986). We evaluated five
mappers using alignment and assignment rates as well as computational time. Alignment
rate was calculated as the ratio of aligned and input reads, while the assignment rate
was calculated as the ratio of assigned and aligned reads. Finally, totals of detected
sRNAs biotypes were compared between different mappers. The statistical analysis was
performed in R (version 4.3.0) and performance metrics are discussed.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles
EP  - 85
SP  - 85
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2030
ER  - 

@conference{
author = "Banović Đeri, Bojana and Nešić, Sofija and Pantelić, Ana and Samardžić, Jelena and Nikolić, Dragana",
year = "2023",
abstract = "Bacterial small RNAs (sRNAs) represent a highly diverse RNA class ranging from 8 to 200
nucleotides in length, originating from the bacterial chromosome, plasmids or phages.
After syntheses sRNAs can remain inside the bacterial cell, be secreted or packed into
outer membrane vesicles (OMV), enabling various intra- and inter-kingdom interactions.
Different sRNAs biotypes display differences in structure, mechanism of action and level
of regulation (i.e. transcription, translation, mRNA stability, etc.), but could be broadly
grouped in: trans-acting sRNAs (bind to target mRNAs) and cis-encoded sRNAs (or
antisense RNA that may interact not only with mRNAs, but also with proteins and DNA).
Even though the advancement of high-throughput sequencing technology led to a burst
of knowledge on small RNAs complexity and diversity, there are still specific challenges
related to sRNA-seq data analysis that need to be resolved. Two main challenges,
associated to short length of many bacterial sRNA biotypes, are: (i) to discriminate
between functional sRNAs synthesized by bacterial cell and degradation fragments
produced by sample preparation and (ii) to detect functional sRNAs displaying sequence
variation. While loss of very small sized sRNAs could easily be overcome by cutting-off
only the specific adapter sequences that were used in sRNA library preparation, providing
a proper mapping still remains a strenuous task.
The aim of this study was to test five different mapping tools that are widely used in NGS
data analysis (bbmap, bowtie2, bwa, minimap2 and segemehl) for their performances in
mapping of bacterial OMV sRNA-seq data to bacterial reference genome. For this test
publicly available NCBI sRNA-seq dataset from OMVs of Aliivibrio fischeri (PRJNA629425)
was used, as it contained sRNAs of different length and biotype and because A.fischeri
reference genome and annotation were available (PRJNA12986). We evaluated five
mappers using alignment and assignment rates as well as computational time. Alignment
rate was calculated as the ratio of aligned and input reads, while the assignment rate
was calculated as the ratio of assigned and aligned reads. Finally, totals of detected
sRNAs biotypes were compared between different mappers. The statistical analysis was
performed in R (version 4.3.0) and performance metrics are discussed.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles",
pages = "85-85",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2030"
}

Banović Đeri, B., Nešić, S., Pantelić, A., Samardžić, J.,& Nikolić, D.. (2023). Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2030

Banović Đeri B, Nešić S, Pantelić A, Samardžić J, Nikolić D. Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles. in 4th Belgrade Bioinformatics Conference. 2023;4:85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2030 .

Banović Đeri, Bojana, Nešić, Sofija, Pantelić, Ana, Samardžić, Jelena, Nikolić, Dragana, "Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles" in 4th Belgrade Bioinformatics Conference, 4 (2023):85-85,
https://hdl.handle.net/21.15107/rcub_imagine_2030 .

TY  - CONF
AU  - Golob, Aleksandra
AU  - Ojdanič, Nik
AU  - Živanović, Bojana
AU  - Germ, Mateja
AU  - Milić Komić, Sonja
AU  - Sedlarević Zorić, Ana
AU  - Milić, Dejana
AU  - Pantelić, Ana
AU  - Mavrič Čermelj, Anja
AU  - Samardžić, Jelena
AU  - Veljovic Jovanovic, Sonja
AU  - Vidović, Marija
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1839
AB  - Drought causes huge agricultural and economic losses worldwide. Silicon (Si) is considered abeneficial element for plants. It mitigates stress caused by salinity, drought, and high and low temperaturesby promoting antioxidant production. However, the underlying mechanisms are still notelucidated. We investigated Si fertilisation effect on photosynthetic parameters, trichome number,leaf optical properties, as well as profiles of amino acids and polyphenols in barley exposed towater shortage. Silicon was applied in three growth stages: (i) before the flag leaf emergence;(ii) prior to the grain filling phase; (iii) at the grain filling phase start. Drought negatively impactsphotochemical efficiency, stomatal conductance, photosynthetic pigment content, and leaf reflectiveand transmissive properties. Si application between flag leaf emergence and grain fillinghad the strongest effect on light reflectance. Among all analyzed phenolics, saponarin was themost abundant in all samples, irrespective of water regime and Si supply. Caffeoyl ester was theonly hydroxycinnamic acid showing significant accumulation with the latest applied Si comparedto no added Si upon drought. The major amino acids in barley leaves were glutamate, glutamine,aspartate, asparagine, and serine. Aspartate content was the highest in leaves exposed to droughtwithout Si addition, while lysine was the most accumulated in the leaves supplemented by Si atthe grain filling phase start. Proline was 2.5 times more abundant in the leaves exposed to droughtregardless of Si treatment. Taken together, although Si did not mitigate drought stress effects, itseffect was dependent on the barley growth phase prior to supplementation.
PB  - Serbian Plant Physiology Society
PB  - Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade
PB  - Faculty of Biology, University of Belgrade
C3  - 4th International Conference on Plant Biology and 23rd SPPS Meeting
T1  - The usage of silicon fertilisation in order to mitigate the oxidative stress and to improve the resilience of barley subjected to drought
SP  - 67
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1839
ER  - 

@conference{
author = "Golob, Aleksandra and Ojdanič, Nik and Živanović, Bojana and Germ, Mateja and Milić Komić, Sonja and Sedlarević Zorić, Ana and Milić, Dejana and Pantelić, Ana and Mavrič Čermelj, Anja and Samardžić, Jelena and Veljovic Jovanovic, Sonja and Vidović, Marija",
year = "2022",
abstract = "Drought causes huge agricultural and economic losses worldwide. Silicon (Si) is considered abeneficial element for plants. It mitigates stress caused by salinity, drought, and high and low temperaturesby promoting antioxidant production. However, the underlying mechanisms are still notelucidated. We investigated Si fertilisation effect on photosynthetic parameters, trichome number,leaf optical properties, as well as profiles of amino acids and polyphenols in barley exposed towater shortage. Silicon was applied in three growth stages: (i) before the flag leaf emergence;(ii) prior to the grain filling phase; (iii) at the grain filling phase start. Drought negatively impactsphotochemical efficiency, stomatal conductance, photosynthetic pigment content, and leaf reflectiveand transmissive properties. Si application between flag leaf emergence and grain fillinghad the strongest effect on light reflectance. Among all analyzed phenolics, saponarin was themost abundant in all samples, irrespective of water regime and Si supply. Caffeoyl ester was theonly hydroxycinnamic acid showing significant accumulation with the latest applied Si comparedto no added Si upon drought. The major amino acids in barley leaves were glutamate, glutamine,aspartate, asparagine, and serine. Aspartate content was the highest in leaves exposed to droughtwithout Si addition, while lysine was the most accumulated in the leaves supplemented by Si atthe grain filling phase start. Proline was 2.5 times more abundant in the leaves exposed to droughtregardless of Si treatment. Taken together, although Si did not mitigate drought stress effects, itseffect was dependent on the barley growth phase prior to supplementation.",
publisher = "Serbian Plant Physiology Society, Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade, Faculty of Biology, University of Belgrade",
journal = "4th International Conference on Plant Biology and 23rd SPPS Meeting",
title = "The usage of silicon fertilisation in order to mitigate the oxidative stress and to improve the resilience of barley subjected to drought",
pages = "67",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1839"
}

Golob, A., Ojdanič, N., Živanović, B., Germ, M., Milić Komić, S., Sedlarević Zorić, A., Milić, D., Pantelić, A., Mavrič Čermelj, A., Samardžić, J., Veljovic Jovanovic, S.,& Vidović, M.. (2022). The usage of silicon fertilisation in order to mitigate the oxidative stress and to improve the resilience of barley subjected to drought. in 4th International Conference on Plant Biology and 23rd SPPS Meeting
Serbian Plant Physiology Society., 67.
https://hdl.handle.net/21.15107/rcub_imagine_1839

Golob A, Ojdanič N, Živanović B, Germ M, Milić Komić S, Sedlarević Zorić A, Milić D, Pantelić A, Mavrič Čermelj A, Samardžić J, Veljovic Jovanovic S, Vidović M. The usage of silicon fertilisation in order to mitigate the oxidative stress and to improve the resilience of barley subjected to drought. in 4th International Conference on Plant Biology and 23rd SPPS Meeting. 2022;:67.
https://hdl.handle.net/21.15107/rcub_imagine_1839 .

Golob, Aleksandra, Ojdanič, Nik, Živanović, Bojana, Germ, Mateja, Milić Komić, Sonja, Sedlarević Zorić, Ana, Milić, Dejana, Pantelić, Ana, Mavrič Čermelj, Anja, Samardžić, Jelena, Veljovic Jovanovic, Sonja, Vidović, Marija, "The usage of silicon fertilisation in order to mitigate the oxidative stress and to improve the resilience of barley subjected to drought" in 4th International Conference on Plant Biology and 23rd SPPS Meeting (2022):67,
https://hdl.handle.net/21.15107/rcub_imagine_1839 .

TY  - CONF
AU  - Milić, Dejana
AU  - Pantelić, Ana
AU  - Banović Đeri, Bojana
AU  - Samardžić, Jelena
AU  - Vidović, Marija
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1848
AB  - In the global warming era, we are facing extreme changes in environmental conditions such
as high and low temperatures, high light and ultraviolet radiation intensity, as well as drought
and increased CO2 levels. The effects of these factors on plants are often interrelated and usually
result in a disturbed balance between the amount of energy received and the ability to process
it. In order to balance energy input and prevent photooxidative damage, plants have evolved
multiple mechanisms for energy dissipation and photoprotection. To efficiently dissipate the excess
excitation energy (EEE), the additional electron sinks, such as photorespiration, biosynthesis
of phenolics and nitrate reduction are stimulated. Variegated leaves of Pelargonium zonale have
been proven to be a suitable model system for examining ‘source–sink’ interactions within the
same leaf, providing the same microenvironment conditions, unlike common root-shoot studies.
The aim of our study was to investigate carbon and nitrogen reallocation between photosynthetically
active (green leaf sectors) and photosynthetically inactive (white leaf sectors) under EEE
pressure induced by low temperature in combination with high light intensity. Besides the amino
acids and phenolics analyses, we monitored morphological and photosynthetic parameters of
P. zonale leaves. Our results revealed higher content of free proteogenic amino acids in the white
leaf sectors than in the green ones. Moreover, EEE triggered increased polyphenol synthesis, namely
anthocyanins, already on the fourth day of the experiment. Also, the leaf fresh/dry weight (FW/
DW) ratio was significantly lower in plants exposed to EEE, indicating possible cell wall stiffening.
PB  - Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade
C3  - 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022
T1  - The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study
SP  - 66
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1848
ER  - 

@conference{
author = "Milić, Dejana and Pantelić, Ana and Banović Đeri, Bojana and Samardžić, Jelena and Vidović, Marija",
year = "2022",
abstract = "In the global warming era, we are facing extreme changes in environmental conditions such
as high and low temperatures, high light and ultraviolet radiation intensity, as well as drought
and increased CO2 levels. The effects of these factors on plants are often interrelated and usually
result in a disturbed balance between the amount of energy received and the ability to process
it. In order to balance energy input and prevent photooxidative damage, plants have evolved
multiple mechanisms for energy dissipation and photoprotection. To efficiently dissipate the excess
excitation energy (EEE), the additional electron sinks, such as photorespiration, biosynthesis
of phenolics and nitrate reduction are stimulated. Variegated leaves of Pelargonium zonale have
been proven to be a suitable model system for examining ‘source–sink’ interactions within the
same leaf, providing the same microenvironment conditions, unlike common root-shoot studies.
The aim of our study was to investigate carbon and nitrogen reallocation between photosynthetically
active (green leaf sectors) and photosynthetically inactive (white leaf sectors) under EEE
pressure induced by low temperature in combination with high light intensity. Besides the amino
acids and phenolics analyses, we monitored morphological and photosynthetic parameters of
P. zonale leaves. Our results revealed higher content of free proteogenic amino acids in the white
leaf sectors than in the green ones. Moreover, EEE triggered increased polyphenol synthesis, namely
anthocyanins, already on the fourth day of the experiment. Also, the leaf fresh/dry weight (FW/
DW) ratio was significantly lower in plants exposed to EEE, indicating possible cell wall stiffening.",
publisher = "Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade",
journal = "4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022",
title = "The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study",
pages = "66",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1848"
}

Milić, D., Pantelić, A., Banović Đeri, B., Samardžić, J.,& Vidović, M.. (2022). The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study. in 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022
Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade., 66.
https://hdl.handle.net/21.15107/rcub_imagine_1848

Milić D, Pantelić A, Banović Đeri B, Samardžić J, Vidović M. The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study. in 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022. 2022;:66.
https://hdl.handle.net/21.15107/rcub_imagine_1848 .

Milić, Dejana, Pantelić, Ana, Banović Đeri, Bojana, Samardžić, Jelena, Vidović, Marija, "The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study" in 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022 (2022):66,
https://hdl.handle.net/21.15107/rcub_imagine_1848 .

TY  - JOUR
AU  - Bačić, Jasmina
AU  - Bosnić, Dragana
AU  - Samardžić, Jelena
AU  - Avdalović, Radmila
AU  - Mickovski-Stefanović, Violeta
AU  - Kušić-Tišma, Jelena
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1543
AB  - Korenove nematode ili nematode korenovih gala mogu prouzrokovati značajne gubitke u prinosu krompira u toplim i hladnim regionima. Šest vrsta Meloidogine mogu parazitirati krompir. Vrste Meloidogyne chitvoodi, M. fallax i M. hapla prisutne su u hladnim regionima, dok su M. arenaria, M. incognita i M. javanica uobičajene u toplim regionima i pripadaju tropskoj grupi Meloidogyne vrsta. Meloidogyne arenaria je prisutna u regionima sa kontinentalnom klimom u zaštićenom prostoru i napada veliki broj biljaka domaćina. U oktobru 2018. primećen je usev krompira var. Balatonska ruža sa tumoroznim izraslinama na 70% krtola tokom posebnog nadzora karantinskih vrsta nematoda Meloidogyne chitvoodi i M. fallax na lokalitetu Horgoš, opština Kanjiža, Pokrajina Vojvodina. Uočeni su i simptomi usporenog rasta i uvenuća biljaka. Ženke su korišćene za morfološku i molekularnu identifikaciju. Morfološka analiza vulvalno-analnih konusa je utvrdila vrstu M. arenaria. Identifikacija vrste je potvrđena molekularnom analizom korišćenjem grupnih specifičnih prajmera u rDNK regionu i SCAR prajmera specifičnih za identifikaciju vrste M. arenaria. Prema našim saznanjima, ovo je prvi nalaz velike štetnosti na krompiru prouzrokovanim prisustvom M. arenaria u polju u Srbiji. Na delu Balkanskog poluostrva sa kontinentalnom klimom nisu ranije zabeležene velike štete usled prisustva M. arenaria na krompiru na otvorenom. Ova tropska vrsta Meloidogyne mogla bi u budućnosti da postane novi fitosanitarni problem u Evropi usled globalnog zagrevanja i klimatskih promena.
AB  - Root-knot nematodes can cause significant losses in potato yield in warm and cool regions. Six Meloidogyne species can attack potato. Species Meloidogyne chitwoodi, M. fallax, M. hapla, are present in cool regions, while M. arenaria, M. incognita and M. javanica are common in warm regions and considered to belong to the Meloidogyne tropical group. Meloidogyne arenaria is present in regions with continental climate in glasshouses attacking a large number of host-plants. In October 2018, potato crop var. Balathon Rose with galls on 70% of all tubers was noticed during quarantine nematode species Meloidogyne chitwoodi and M. fallax survey in the locality Horgoš, municipality of Kanjiža, Vojvodina Province. Symptoms of stunted and wilted plants were detected as well. Females were used for morphological and molecular identification. Morphological identification of species based on females' perineal patterns indicated the sample as M. arenaria. Species identification was confirmed by molecular analyses using group-specific primers in the rDNA region and species-specific SCAR primers for M. arenaria species identification. To our knowledge, this is the first record of highly damaged potato crop caused by M. arenaria in the field in Serbia. The severity of the damage M. arenaria can cause to potato in the open field has not been observed in the part of Balkan peninsula with continental climate before. This tropical Meloidogyne species may become an emerging phytosanitary problem within Europe in the future due global warming and climate change.
PB  - Institut za ratarstvo i povrtarstvo, Novi Sad
T2  - Ratarstvo i Povrtarstvo
T1  - Prisustvo korenove nematode Meloidogyne arenaria na krompiru u polju u Srbiji
T1  - Occurrence of root-knot nematode Meloidogyne arenaria in the potato field in Serbia
EP  - 55
IS  - 2
SP  - 51
VL  - 59
DO  - 10.5937/ratpov59-38187
ER  - 

@article{
author = "Bačić, Jasmina and Bosnić, Dragana and Samardžić, Jelena and Avdalović, Radmila and Mickovski-Stefanović, Violeta and Kušić-Tišma, Jelena",
year = "2022",
abstract = "Korenove nematode ili nematode korenovih gala mogu prouzrokovati značajne gubitke u prinosu krompira u toplim i hladnim regionima. Šest vrsta Meloidogine mogu parazitirati krompir. Vrste Meloidogyne chitvoodi, M. fallax i M. hapla prisutne su u hladnim regionima, dok su M. arenaria, M. incognita i M. javanica uobičajene u toplim regionima i pripadaju tropskoj grupi Meloidogyne vrsta. Meloidogyne arenaria je prisutna u regionima sa kontinentalnom klimom u zaštićenom prostoru i napada veliki broj biljaka domaćina. U oktobru 2018. primećen je usev krompira var. Balatonska ruža sa tumoroznim izraslinama na 70% krtola tokom posebnog nadzora karantinskih vrsta nematoda Meloidogyne chitvoodi i M. fallax na lokalitetu Horgoš, opština Kanjiža, Pokrajina Vojvodina. Uočeni su i simptomi usporenog rasta i uvenuća biljaka. Ženke su korišćene za morfološku i molekularnu identifikaciju. Morfološka analiza vulvalno-analnih konusa je utvrdila vrstu M. arenaria. Identifikacija vrste je potvrđena molekularnom analizom korišćenjem grupnih specifičnih prajmera u rDNK regionu i SCAR prajmera specifičnih za identifikaciju vrste M. arenaria. Prema našim saznanjima, ovo je prvi nalaz velike štetnosti na krompiru prouzrokovanim prisustvom M. arenaria u polju u Srbiji. Na delu Balkanskog poluostrva sa kontinentalnom klimom nisu ranije zabeležene velike štete usled prisustva M. arenaria na krompiru na otvorenom. Ova tropska vrsta Meloidogyne mogla bi u budućnosti da postane novi fitosanitarni problem u Evropi usled globalnog zagrevanja i klimatskih promena., Root-knot nematodes can cause significant losses in potato yield in warm and cool regions. Six Meloidogyne species can attack potato. Species Meloidogyne chitwoodi, M. fallax, M. hapla, are present in cool regions, while M. arenaria, M. incognita and M. javanica are common in warm regions and considered to belong to the Meloidogyne tropical group. Meloidogyne arenaria is present in regions with continental climate in glasshouses attacking a large number of host-plants. In October 2018, potato crop var. Balathon Rose with galls on 70% of all tubers was noticed during quarantine nematode species Meloidogyne chitwoodi and M. fallax survey in the locality Horgoš, municipality of Kanjiža, Vojvodina Province. Symptoms of stunted and wilted plants were detected as well. Females were used for morphological and molecular identification. Morphological identification of species based on females' perineal patterns indicated the sample as M. arenaria. Species identification was confirmed by molecular analyses using group-specific primers in the rDNA region and species-specific SCAR primers for M. arenaria species identification. To our knowledge, this is the first record of highly damaged potato crop caused by M. arenaria in the field in Serbia. The severity of the damage M. arenaria can cause to potato in the open field has not been observed in the part of Balkan peninsula with continental climate before. This tropical Meloidogyne species may become an emerging phytosanitary problem within Europe in the future due global warming and climate change.",
publisher = "Institut za ratarstvo i povrtarstvo, Novi Sad",
journal = "Ratarstvo i Povrtarstvo",
title = "Prisustvo korenove nematode Meloidogyne arenaria na krompiru u polju u Srbiji, Occurrence of root-knot nematode Meloidogyne arenaria in the potato field in Serbia",
pages = "55-51",
number = "2",
volume = "59",
doi = "10.5937/ratpov59-38187"
}

Bačić, J., Bosnić, D., Samardžić, J., Avdalović, R., Mickovski-Stefanović, V.,& Kušić-Tišma, J.. (2022). Prisustvo korenove nematode Meloidogyne arenaria na krompiru u polju u Srbiji. in Ratarstvo i Povrtarstvo
Institut za ratarstvo i povrtarstvo, Novi Sad., 59(2), 51-55.
https://doi.org/10.5937/ratpov59-38187

Bačić J, Bosnić D, Samardžić J, Avdalović R, Mickovski-Stefanović V, Kušić-Tišma J. Prisustvo korenove nematode Meloidogyne arenaria na krompiru u polju u Srbiji. in Ratarstvo i Povrtarstvo. 2022;59(2):51-55.
doi:10.5937/ratpov59-38187 .

Bačić, Jasmina, Bosnić, Dragana, Samardžić, Jelena, Avdalović, Radmila, Mickovski-Stefanović, Violeta, Kušić-Tišma, Jelena, "Prisustvo korenove nematode Meloidogyne arenaria na krompiru u polju u Srbiji" in Ratarstvo i Povrtarstvo, 59, no. 2 (2022):51-55,
https://doi.org/10.5937/ratpov59-38187 . .

TY  - JOUR
AU  - Banović Đeri, Bojana
AU  - Bozić, Manja
AU  - Dudić, Dragana
AU  - Vicić, Ivan
AU  - Milivojević, Marija
AU  - Ignjatović-Micić, Dragana
AU  - Samardžić, Jelena
AU  - Vancetović, Jelena
AU  - Delić, Nenad
AU  - Nikolić, Ana
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1576
AB  - One of the strategies for overcoming global climate change threatening to decrease maize yield is early sowing. To contribute to the development of cold-tolerant hybrids this research focused on the genetic background's comparative analysis in maize inbreds with good combining ability. Leaf whole-transcriptome sequencing of 46 maize genotypes revealed 77 differentially expressed genes (DEGs) between Lancaster and other heterotic groups (i.e. BSSS, Iowa dent, Ohio), referred to as non-Lancaster group, under optimal growing conditions. Cold test of the subset of four Lancaster and four non-Lancaster lines showed that the former were cold sensitive and the latter cold tolerant. Cold-induced expression analysis of seven DEGs in eight lines revealed different expression regulation dependent on the duration of cold exposure and genetic background for six out of seven analysed genes-chloroplast ATP-sulphurylase, photosystem II cytochrome b559 alpha subunit, CIPK serine-threonine protein kinase 15, glutamyl-tRNA reductase, photosystem II reaction centre protein I and Calvin cycle CP12-chloroplastic-like encoding genes. The results imply that differently regulated basic processes between Lancaster and non-Lancaster maize group involve, at least, photosynthesis and sulphate assimilation, contributing to their different cold response and different adaptation to low temperatures.
PB  - Wiley, Hoboken
T2  - Journal of Agronomy and Crop Science
T1  - Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes
EP  - 509
IS  - 4
SP  - 497
VL  - 208
DO  - 10.1111/jac.12529
ER  - 

@article{
author = "Banović Đeri, Bojana and Bozić, Manja and Dudić, Dragana and Vicić, Ivan and Milivojević, Marija and Ignjatović-Micić, Dragana and Samardžić, Jelena and Vancetović, Jelena and Delić, Nenad and Nikolić, Ana",
year = "2022",
abstract = "One of the strategies for overcoming global climate change threatening to decrease maize yield is early sowing. To contribute to the development of cold-tolerant hybrids this research focused on the genetic background's comparative analysis in maize inbreds with good combining ability. Leaf whole-transcriptome sequencing of 46 maize genotypes revealed 77 differentially expressed genes (DEGs) between Lancaster and other heterotic groups (i.e. BSSS, Iowa dent, Ohio), referred to as non-Lancaster group, under optimal growing conditions. Cold test of the subset of four Lancaster and four non-Lancaster lines showed that the former were cold sensitive and the latter cold tolerant. Cold-induced expression analysis of seven DEGs in eight lines revealed different expression regulation dependent on the duration of cold exposure and genetic background for six out of seven analysed genes-chloroplast ATP-sulphurylase, photosystem II cytochrome b559 alpha subunit, CIPK serine-threonine protein kinase 15, glutamyl-tRNA reductase, photosystem II reaction centre protein I and Calvin cycle CP12-chloroplastic-like encoding genes. The results imply that differently regulated basic processes between Lancaster and non-Lancaster maize group involve, at least, photosynthesis and sulphate assimilation, contributing to their different cold response and different adaptation to low temperatures.",
publisher = "Wiley, Hoboken",
journal = "Journal of Agronomy and Crop Science",
title = "Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes",
pages = "509-497",
number = "4",
volume = "208",
doi = "10.1111/jac.12529"
}

Banović Đeri, B., Bozić, M., Dudić, D., Vicić, I., Milivojević, M., Ignjatović-Micić, D., Samardžić, J., Vancetović, J., Delić, N.,& Nikolić, A.. (2022). Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes. in Journal of Agronomy and Crop Science
Wiley, Hoboken., 208(4), 497-509.
https://doi.org/10.1111/jac.12529

Banović Đeri B, Bozić M, Dudić D, Vicić I, Milivojević M, Ignjatović-Micić D, Samardžić J, Vancetović J, Delić N, Nikolić A. Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes. in Journal of Agronomy and Crop Science. 2022;208(4):497-509.
doi:10.1111/jac.12529 .

Banović Đeri, Bojana, Bozić, Manja, Dudić, Dragana, Vicić, Ivan, Milivojević, Marija, Ignjatović-Micić, Dragana, Samardžić, Jelena, Vancetović, Jelena, Delić, Nenad, Nikolić, Ana, "Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes" in Journal of Agronomy and Crop Science, 208, no. 4 (2022):497-509,
https://doi.org/10.1111/jac.12529 . .

TY  - CONF
AU  - Vidović, Marija
AU  - Banović Đeri, Bojana
AU  - Samardžić, Jelena
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1873
AB  - Variegated Pelargonium zonale leaves have proven to be an excellent model system to examine source–sink
interactions within the same organ providing the equal microenvironment conditions, unlike common shoot/
root relation studies. Photosynthetically non-active (W) mesophyll cells contain smaller plastids lacking thylakoid
membranes or starch granules, and exhibit no peroxisomes in comparison to photosynthetically active
(G) cells. With the aim of gaining a deeper insight into molecular phenotype of W leaf tissue, particularly
the one related to photosynthetic-dependent H2O2 metabolism, transcriptomes of these two metabolically
contrasted tissues were compared.
High-quality total RNA from W and G leaf tissues was extracted according to our previously optimised
protocol. Highly purified cDNA libraries were synthesized and sequenced on an Illumina platform. The
ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed and the read quality
was checked before and after the trimming. In total, 39763284 (with Q30=94.3%) and 42062153 (with
Q30=94.0%) clean reads were obtained in G and W total RNA samples, respectively, and used to perform
transcriptome assembly by Trinity software. After removing the redundancy, via Corset software, 139811
transcripts with 139575 unigenes were annotated through comparison with seven commonly used databases
(NCBI non-redundant protein and nucleotide sequences; PFAM; Clusters of Orthologous Groups of proteins,
Swiss-Prot, KEGG, GO).
Analysis of differentially expressed genes was performed using DESeq2 R package and revealed 4668 upregulated
genes and 6689 down-regulated genes in G tissue compared with W one. Among the up-regulated
genes in G tissue, the majority was associated with cytoskeleton, photosynthetic processes, plastids, thylakoids
and transport, while in W tissue up-regulated genes were mainly found to encode enzymes with ATPase
activity, carbohydrate absorption and digestion, callose, pectin and linoleic acid metabolism. Moreover, a significant
difference between these two tissues differing in H2O2 generation rate was observed in the expression
level of genes involved in H2O2 scavenging. Enzymatic constituents of the ascorbate-glutathione cycle and
glutathione-S-transferase were up-regulated in W tissue, while catalase, glutathione-peroxidases and three
Class III peroxidases were all up-regulated in G tissue. The obtained transcriptome results were correlated
with previously revealed morphological, biochemical, and molecular characteristics of these two tissues.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves
IS  - 1 (Special Edition)
SP  - 107
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1873
ER  - 

@conference{
author = "Vidović, Marija and Banović Đeri, Bojana and Samardžić, Jelena",
year = "2021",
abstract = "Variegated Pelargonium zonale leaves have proven to be an excellent model system to examine source–sink
interactions within the same organ providing the equal microenvironment conditions, unlike common shoot/
root relation studies. Photosynthetically non-active (W) mesophyll cells contain smaller plastids lacking thylakoid
membranes or starch granules, and exhibit no peroxisomes in comparison to photosynthetically active
(G) cells. With the aim of gaining a deeper insight into molecular phenotype of W leaf tissue, particularly
the one related to photosynthetic-dependent H2O2 metabolism, transcriptomes of these two metabolically
contrasted tissues were compared.
High-quality total RNA from W and G leaf tissues was extracted according to our previously optimised
protocol. Highly purified cDNA libraries were synthesized and sequenced on an Illumina platform. The
ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed and the read quality
was checked before and after the trimming. In total, 39763284 (with Q30=94.3%) and 42062153 (with
Q30=94.0%) clean reads were obtained in G and W total RNA samples, respectively, and used to perform
transcriptome assembly by Trinity software. After removing the redundancy, via Corset software, 139811
transcripts with 139575 unigenes were annotated through comparison with seven commonly used databases
(NCBI non-redundant protein and nucleotide sequences; PFAM; Clusters of Orthologous Groups of proteins,
Swiss-Prot, KEGG, GO).
Analysis of differentially expressed genes was performed using DESeq2 R package and revealed 4668 upregulated
genes and 6689 down-regulated genes in G tissue compared with W one. Among the up-regulated
genes in G tissue, the majority was associated with cytoskeleton, photosynthetic processes, plastids, thylakoids
and transport, while in W tissue up-regulated genes were mainly found to encode enzymes with ATPase
activity, carbohydrate absorption and digestion, callose, pectin and linoleic acid metabolism. Moreover, a significant
difference between these two tissues differing in H2O2 generation rate was observed in the expression
level of genes involved in H2O2 scavenging. Enzymatic constituents of the ascorbate-glutathione cycle and
glutathione-S-transferase were up-regulated in W tissue, while catalase, glutathione-peroxidases and three
Class III peroxidases were all up-regulated in G tissue. The obtained transcriptome results were correlated
with previously revealed morphological, biochemical, and molecular characteristics of these two tissues.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves",
number = "1 (Special Edition)",
pages = "107",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1873"
}

Vidović, M., Banović Đeri, B.,& Samardžić, J.. (2021). Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves. in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 107.
https://hdl.handle.net/21.15107/rcub_imagine_1873

Vidović M, Banović Đeri B, Samardžić J. Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves. in Biologia Serbica. 2021;43(1 (Special Edition)):107.
https://hdl.handle.net/21.15107/rcub_imagine_1873 .

Vidović, Marija, Banović Đeri, Bojana, Samardžić, Jelena, "Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):107,
https://hdl.handle.net/21.15107/rcub_imagine_1873 .

TY  - CONF
AU  - Božić, Manja
AU  - Nikolić, Ana
AU  - Dudić, Dragana
AU  - Ignjatović-Micić, Dragana
AU  - Samardžić, Jelena
AU  - Delić, Nenad
AU  - Banović Đeri, Bojana
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1874
AB  - Finding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most
important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction
is climate change, specifically increasing temperatures and drought during the summer, a large number of
strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing
(early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding
high summer temperatures. Thus, development of cold tolerant maize lines became an important goal.
Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly
cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as
Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE)
analysis. Plants were grown under optimal, greenhouse conditions and sampled after completing the V4
growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation
by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina
sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a
custom-made bioinformatics pipeline that included high throughput sequence data quality control (using
FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and
mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using
BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2).
DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster
group, 21 of which were statistically supported for differential expression between the two groups and
annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to
cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging
to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4°
C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after
48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and
genetic background. These findings imply differently regulated processes between the analysed Lancaster
and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be
further used for the development of cold tolerant hybrids.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature
IS  - 1 (Special Edition)
SP  - 106
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1874
ER  - 

@conference{
author = "Božić, Manja and Nikolić, Ana and Dudić, Dragana and Ignjatović-Micić, Dragana and Samardžić, Jelena and Delić, Nenad and Banović Đeri, Bojana",
year = "2021",
abstract = "Finding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most
important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction
is climate change, specifically increasing temperatures and drought during the summer, a large number of
strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing
(early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding
high summer temperatures. Thus, development of cold tolerant maize lines became an important goal.
Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly
cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as
Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE)
analysis. Plants were grown under optimal, greenhouse conditions and sampled after completing the V4
growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation
by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina
sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a
custom-made bioinformatics pipeline that included high throughput sequence data quality control (using
FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and
mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using
BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2).
DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster
group, 21 of which were statistically supported for differential expression between the two groups and
annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to
cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging
to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4°
C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after
48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and
genetic background. These findings imply differently regulated processes between the analysed Lancaster
and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be
further used for the development of cold tolerant hybrids.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature",
number = "1 (Special Edition)",
pages = "106",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1874"
}

Božić, M., Nikolić, A., Dudić, D., Ignjatović-Micić, D., Samardžić, J., Delić, N.,& Banović Đeri, B.. (2021). Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature. in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 106.
https://hdl.handle.net/21.15107/rcub_imagine_1874

Božić M, Nikolić A, Dudić D, Ignjatović-Micić D, Samardžić J, Delić N, Banović Đeri B. Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature. in Biologia Serbica. 2021;43(1 (Special Edition)):106.
https://hdl.handle.net/21.15107/rcub_imagine_1874 .

Božić, Manja, Nikolić, Ana, Dudić, Dragana, Ignjatović-Micić, Dragana, Samardžić, Jelena, Delić, Nenad, Banović Đeri, Bojana, "Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):106,
https://hdl.handle.net/21.15107/rcub_imagine_1874 .

TY  - CHAP
AU  - Bosnić, Dragana
AU  - Nikolić, Dragana
AU  - Samardžić, Jelena
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1717
AB  - Bakar (Cu) je esencijalan mikroelement za biljke ali ukoliko je prisutan u višku ima fitotoksično
dejstvo izazivajući oksidativni stres. Silicijum(Si) ne spada u esencijalne ali je jedini element koji ispoljava protektivan
efekat na biljke u uslovima stresa. Primena silicijumove kiseline kod biljaka tretiranih toksičnim koncentracijama
bakra ublažava štetna dejstva i povećava toleranciju na prisustvo bakra u višku. Mehanizmi
delovanja silicijuma kod biljaka krastavca su detaljno proučeni i obuhvataju: smanjenje akumulacije Cu u
biljkama preko snižene ekspresije gena odgovornih za njegovo usvajanje, imobilizaciju Cu u ćelijskim zidovima,
povećanje sinteze Cu-liganada: organskih kiselina (citrat, malat i akonitat) i aminokiselina (nikocijanamin
i histidin) koji smanjuju koncentraciju slobodnih, reaktivnih jona Cu unutar ćelije. Primena Si je
uslovila smanjenje ekspresije mikro RNK (miR398 i miR408) koje predstavljaju glavne regulatore ekspresije
gena i proteina koji sadrže Cu kao kofaktor. Posledično, akumulacija Cu-proteina Cu/Zn superoksid-dismutaze
i plastocijanina koji vezujući Cu doprinose skladištenju viška jona Cu u biljnim ćelijama, je izraženija
kod biljaka gajenih sa silicijumom. Razumevanje uloge i mehanizama delovanja Si u biljkama će doprineti
njegovoj širokoj praktičnoj primeni u cilju povećanja rezistencije i tolerancije biljaka na stres.
AB  - Although copper (Cu) is an essential microelement for plants, if present in excess it has a phytotoxic
effect causing oxidative stress. Silicon (Si) is not essential, but it is the only element with protective effect
to plants under stress. Application of silicic acid to plants treated with toxic concentrations of copper
alleviates the harmful effects of excess copper, which results in increase tolerance in these plants. The protective
mechanisms of Si in cucumber plants have been studied in more details and include a decrease in
accumulation of Cu by downregulation of genes responsible for Cu uptake in plants, immobilization of Cu
in the root cell walls as well as higher biosynthesis of Cu-ligands: organic acids (citrate, malate and aconitate)
and amino acids (nicotianamine and histidine) that decrease the concentration of free, reactive Cu ions
within the cell. The application of Si caused lower expression of microRNAs (miR398 and miR408) which are
the main regulators of the expression of genes and proteins containing Cu as a cofactor. Consequently, the
accumulation of Cu-proteins: Cu/Zn superoxide dismutase and plastocyanin, which are buffering sinks for
excess Cu ions in plant cells, is more pronounced in plants grown with silicon. Better understanding the Simediated
mechanisms in plants exposed to stress will contribute to its wider agronomic application in order
to increase plant resistance and tolerance to stress.
PB  - Beograd : Institut za molekularnu genetiku i genetičko inženjerstvo
T2  - Trendovi u molekularnoj Biologiji
T1  - Silicijum kao antistres element za biljke izložene toksičnim koncentracijama bakra
T1  - Silicon as an anti-stress element for plants exposed to toxic copper
EP  - 192
SP  - 180
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1717
ER  - 

@inbook{
author = "Bosnić, Dragana and Nikolić, Dragana and Samardžić, Jelena",
year = "2021",
abstract = "Bakar (Cu) je esencijalan mikroelement za biljke ali ukoliko je prisutan u višku ima fitotoksično
dejstvo izazivajući oksidativni stres. Silicijum(Si) ne spada u esencijalne ali je jedini element koji ispoljava protektivan
efekat na biljke u uslovima stresa. Primena silicijumove kiseline kod biljaka tretiranih toksičnim koncentracijama
bakra ublažava štetna dejstva i povećava toleranciju na prisustvo bakra u višku. Mehanizmi
delovanja silicijuma kod biljaka krastavca su detaljno proučeni i obuhvataju: smanjenje akumulacije Cu u
biljkama preko snižene ekspresije gena odgovornih za njegovo usvajanje, imobilizaciju Cu u ćelijskim zidovima,
povećanje sinteze Cu-liganada: organskih kiselina (citrat, malat i akonitat) i aminokiselina (nikocijanamin
i histidin) koji smanjuju koncentraciju slobodnih, reaktivnih jona Cu unutar ćelije. Primena Si je
uslovila smanjenje ekspresije mikro RNK (miR398 i miR408) koje predstavljaju glavne regulatore ekspresije
gena i proteina koji sadrže Cu kao kofaktor. Posledično, akumulacija Cu-proteina Cu/Zn superoksid-dismutaze
i plastocijanina koji vezujući Cu doprinose skladištenju viška jona Cu u biljnim ćelijama, je izraženija
kod biljaka gajenih sa silicijumom. Razumevanje uloge i mehanizama delovanja Si u biljkama će doprineti
njegovoj širokoj praktičnoj primeni u cilju povećanja rezistencije i tolerancije biljaka na stres., Although copper (Cu) is an essential microelement for plants, if present in excess it has a phytotoxic
effect causing oxidative stress. Silicon (Si) is not essential, but it is the only element with protective effect
to plants under stress. Application of silicic acid to plants treated with toxic concentrations of copper
alleviates the harmful effects of excess copper, which results in increase tolerance in these plants. The protective
mechanisms of Si in cucumber plants have been studied in more details and include a decrease in
accumulation of Cu by downregulation of genes responsible for Cu uptake in plants, immobilization of Cu
in the root cell walls as well as higher biosynthesis of Cu-ligands: organic acids (citrate, malate and aconitate)
and amino acids (nicotianamine and histidine) that decrease the concentration of free, reactive Cu ions
within the cell. The application of Si caused lower expression of microRNAs (miR398 and miR408) which are
the main regulators of the expression of genes and proteins containing Cu as a cofactor. Consequently, the
accumulation of Cu-proteins: Cu/Zn superoxide dismutase and plastocyanin, which are buffering sinks for
excess Cu ions in plant cells, is more pronounced in plants grown with silicon. Better understanding the Simediated
mechanisms in plants exposed to stress will contribute to its wider agronomic application in order
to increase plant resistance and tolerance to stress.",
publisher = "Beograd : Institut za molekularnu genetiku i genetičko inženjerstvo",
journal = "Trendovi u molekularnoj Biologiji",
booktitle = "Silicijum kao antistres element za biljke izložene toksičnim koncentracijama bakra, Silicon as an anti-stress element for plants exposed to toxic copper",
pages = "192-180",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1717"
}

Bosnić, D., Nikolić, D.,& Samardžić, J.. (2021). Silicijum kao antistres element za biljke izložene toksičnim koncentracijama bakra. in Trendovi u molekularnoj Biologiji
Beograd : Institut za molekularnu genetiku i genetičko inženjerstvo., 180-192.
https://hdl.handle.net/21.15107/rcub_imagine_1717

Bosnić D, Nikolić D, Samardžić J. Silicijum kao antistres element za biljke izložene toksičnim koncentracijama bakra. in Trendovi u molekularnoj Biologiji. 2021;:180-192.
https://hdl.handle.net/21.15107/rcub_imagine_1717 .

Bosnić, Dragana, Nikolić, Dragana, Samardžić, Jelena, "Silicijum kao antistres element za biljke izložene toksičnim koncentracijama bakra" in Trendovi u molekularnoj Biologiji (2021):180-192,
https://hdl.handle.net/21.15107/rcub_imagine_1717 .

TY  - JOUR
AU  - Nikolić, Ivana
AU  - Nešić, Sofija
AU  - Samardžić, Jelena
AU  - Timotijević, Gordana
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1487
AB  - DSS1 is a small protein, highly conserved across different species. As a member of the intrinsically disordered protein family, DSS1 interacts with different protein partners, thus forming complexes involved in diverse biological mechanisms: DNA repair, regulation of protein homeostasis, mRNA export, etc. Additionally, DSS1 has a novel intriguing role in the post-translational protein modification named DSSylation. Oxidatively damaged proteins are targeted for removal with DSS1 and then degraded by proteasome. Yet, DSS1 involvement in the maintenance of genome integrity through homologous recombination is the only function well studied in Arabidopsis research. The fact that animal DSS1 shows wide multifunctionality imposes a need to investigate the additional roles of two Arabidopsis thaliana DSS1 homologs. Having in mind the universality of various biological processes, we considered the possibility of plant DSS1 involvement in cellular homeostasis maintenance during stress exposure. Using real-time PCR and immunoblot analysis, we investigated the profiles of DSS1 gene and protein expression under oxidative stress. We grew and selected the homozygous Arabidopsis mutant line, carrying the T-DNA intron insertion in the DSS1(V) gene. The mutant line was phenotypically described during plant development, and its sensitivity to oxidative stress was characterized. This is the first report which indicates that plant DSS1 gene expression has an altered profile under the influence of oxidative stress. dss1(V)(-/-) plants showed an increased sensitivity to oxidative stress, germinated faster than WT, but generally showed developmental delay in further stages. Our results indicate that the DSS1 protein could be a crucial player in the molecular mechanisms underlying plant abiotic stress responses.
PB  - Springer Wien, Wien
T2  - Protoplasma
T1  - Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress
EP  - 792
IS  - 4
SP  - 779
VL  - 258
DO  - 10.1007/s00709-020-01598-7
ER  - 

@article{
author = "Nikolić, Ivana and Nešić, Sofija and Samardžić, Jelena and Timotijević, Gordana",
year = "2021",
abstract = "DSS1 is a small protein, highly conserved across different species. As a member of the intrinsically disordered protein family, DSS1 interacts with different protein partners, thus forming complexes involved in diverse biological mechanisms: DNA repair, regulation of protein homeostasis, mRNA export, etc. Additionally, DSS1 has a novel intriguing role in the post-translational protein modification named DSSylation. Oxidatively damaged proteins are targeted for removal with DSS1 and then degraded by proteasome. Yet, DSS1 involvement in the maintenance of genome integrity through homologous recombination is the only function well studied in Arabidopsis research. The fact that animal DSS1 shows wide multifunctionality imposes a need to investigate the additional roles of two Arabidopsis thaliana DSS1 homologs. Having in mind the universality of various biological processes, we considered the possibility of plant DSS1 involvement in cellular homeostasis maintenance during stress exposure. Using real-time PCR and immunoblot analysis, we investigated the profiles of DSS1 gene and protein expression under oxidative stress. We grew and selected the homozygous Arabidopsis mutant line, carrying the T-DNA intron insertion in the DSS1(V) gene. The mutant line was phenotypically described during plant development, and its sensitivity to oxidative stress was characterized. This is the first report which indicates that plant DSS1 gene expression has an altered profile under the influence of oxidative stress. dss1(V)(-/-) plants showed an increased sensitivity to oxidative stress, germinated faster than WT, but generally showed developmental delay in further stages. Our results indicate that the DSS1 protein could be a crucial player in the molecular mechanisms underlying plant abiotic stress responses.",
publisher = "Springer Wien, Wien",
journal = "Protoplasma",
title = "Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress",
pages = "792-779",
number = "4",
volume = "258",
doi = "10.1007/s00709-020-01598-7"
}

Nikolić, I., Nešić, S., Samardžić, J.,& Timotijević, G.. (2021). Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress. in Protoplasma
Springer Wien, Wien., 258(4), 779-792.
https://doi.org/10.1007/s00709-020-01598-7

Nikolić I, Nešić S, Samardžić J, Timotijević G. Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress. in Protoplasma. 2021;258(4):779-792.
doi:10.1007/s00709-020-01598-7 .

Nikolić, Ivana, Nešić, Sofija, Samardžić, Jelena, Timotijević, Gordana, "Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress" in Protoplasma, 258, no. 4 (2021):779-792,
https://doi.org/10.1007/s00709-020-01598-7 . .

TY  - JOUR
AU  - Karalija, Erna
AU  - Selović, Alisa
AU  - Dahija, Sabina
AU  - Demir, Arnela
AU  - Samardžić, Jelena
AU  - Vrobel, Ondrej
AU  - Cavar-Zeljković, Sanja
AU  - Parić, Adisa
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1488
AB  - Changes in the environment as a result of industrialisation and urbanisation impact negatively on plant growth and crop production. Cadmium (Cd) is one of the most dangerous metals that enters the food chain, with toxic effects on plants and human health. This study evaluated the potential of Silene sendtneri as a novel hyperaccumulator and the role of seed priming in tolerance and accumulation rate of Cd. The effect of different priming agents on germination performance, root growth, seedling development, metal uptake and accumulation, antioxidant defences including enzymatic and non-enzymatic antioxidants has been assessed. Seed priming using silicic acid, proline alone or in combination with salicylic acidenhanced germination, seedling development, and root growth under Cd stress. The same priming treatments induced an increase of water content in shoots and roots when plants were exposed to Cd. The enzymatic antioxidant response was specific for the priming agent used. An increase in ferulic acid and rutin in shoots was related to the increase of Cd concentration in the medium. The concentration of malic and oxalic acid increased significantly in shoots of plants grown on high Cd concentrations compared to low Cd concentrations. Silene sendtneri can accumulate significant levels of Cd with enhanced accumulation rate and tolerance when seeds are primed. The best results are obtained by seed priming using 1% silicic acid, proline and salicylic acid.
PB  - Academic Press Inc Elsevier Science, San Diego
T2  - Ecotoxicology and Environmental Safety
T1  - Use of seed priming to improve Cd accumulation and tolerance in Silene sendtneri, novel Cd hyper-accumulator
VL  - 210
DO  - 10.1016/j.ecoenv.2020.111882
ER  - 

@article{
author = "Karalija, Erna and Selović, Alisa and Dahija, Sabina and Demir, Arnela and Samardžić, Jelena and Vrobel, Ondrej and Cavar-Zeljković, Sanja and Parić, Adisa",
year = "2021",
abstract = "Changes in the environment as a result of industrialisation and urbanisation impact negatively on plant growth and crop production. Cadmium (Cd) is one of the most dangerous metals that enters the food chain, with toxic effects on plants and human health. This study evaluated the potential of Silene sendtneri as a novel hyperaccumulator and the role of seed priming in tolerance and accumulation rate of Cd. The effect of different priming agents on germination performance, root growth, seedling development, metal uptake and accumulation, antioxidant defences including enzymatic and non-enzymatic antioxidants has been assessed. Seed priming using silicic acid, proline alone or in combination with salicylic acidenhanced germination, seedling development, and root growth under Cd stress. The same priming treatments induced an increase of water content in shoots and roots when plants were exposed to Cd. The enzymatic antioxidant response was specific for the priming agent used. An increase in ferulic acid and rutin in shoots was related to the increase of Cd concentration in the medium. The concentration of malic and oxalic acid increased significantly in shoots of plants grown on high Cd concentrations compared to low Cd concentrations. Silene sendtneri can accumulate significant levels of Cd with enhanced accumulation rate and tolerance when seeds are primed. The best results are obtained by seed priming using 1% silicic acid, proline and salicylic acid.",
publisher = "Academic Press Inc Elsevier Science, San Diego",
journal = "Ecotoxicology and Environmental Safety",
title = "Use of seed priming to improve Cd accumulation and tolerance in Silene sendtneri, novel Cd hyper-accumulator",
volume = "210",
doi = "10.1016/j.ecoenv.2020.111882"
}

Karalija, E., Selović, A., Dahija, S., Demir, A., Samardžić, J., Vrobel, O., Cavar-Zeljković, S.,& Parić, A.. (2021). Use of seed priming to improve Cd accumulation and tolerance in Silene sendtneri, novel Cd hyper-accumulator. in Ecotoxicology and Environmental Safety
Academic Press Inc Elsevier Science, San Diego., 210.
https://doi.org/10.1016/j.ecoenv.2020.111882

Karalija E, Selović A, Dahija S, Demir A, Samardžić J, Vrobel O, Cavar-Zeljković S, Parić A. Use of seed priming to improve Cd accumulation and tolerance in Silene sendtneri, novel Cd hyper-accumulator. in Ecotoxicology and Environmental Safety. 2021;210.
doi:10.1016/j.ecoenv.2020.111882 .

Karalija, Erna, Selović, Alisa, Dahija, Sabina, Demir, Arnela, Samardžić, Jelena, Vrobel, Ondrej, Cavar-Zeljković, Sanja, Parić, Adisa, "Use of seed priming to improve Cd accumulation and tolerance in Silene sendtneri, novel Cd hyper-accumulator" in Ecotoxicology and Environmental Safety, 210 (2021),
https://doi.org/10.1016/j.ecoenv.2020.111882 . .

TY  - JOUR
AU  - Stanisavljević, Nemanja
AU  - Soković Bajić, Svetlana
AU  - Jovanović, Živko
AU  - Matić, Ivana
AU  - Tolinački, Maja
AU  - Popović, Dušanka
AU  - Popović, Nikola
AU  - Terzić-Vidojević, Amarela
AU  - Golić, Nataša
AU  - Beskoski, Vladimir
AU  - Samardžić, Jelena
PY  - 2020
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1337
AB  - In this study, for the first time, the comprehensive analysis of antiproliferative and antioxidant activities of ramson, followed by the analysis of its associated microbiota and health-promoting effects of lactic acid bacteria (LAB), was performed. Ramson (Allium ursinum) is recognized as a medicinal plant with a long history of use in traditional medicine due to its antimicrobial and antioxidant activity. In this study the influence of in vitro gastrointestinal digestion on the cytotoxic activity of A. ursinum extracts against human malignant cell lines was demonstrated. Seven sulfur compounds, the degradation products of thiosulfinates, including diallyl disulfide were shown to inhibit proliferation of malignant cells by inducing accumulation within G2/M phase as well as to induce apoptosis through activation of caspase-3 and mitochondrial signaling pathway. Further, the A. ursinum microbiota, particularly LAB with potential probiotic effects, was analyzed by culture-dependent method and culture-independent method [denaturing gradient gel electrophoresis (DGGE)]. The obtained results revealed that the most abundant genera were Streptococcus, Lactobacillus, and Bacillus. The Lactobacillus genus was mainly represented by L. fermentum. The pulsed-field gel electrophoresis (PFGE) analysis revealed the presence of two PFGE pulsotypes. The probiotic potential of the strain L. fermentum BGSR163 belonging to PFGE pulsotype 1 and the strain L. fermentum BGSR227 belonging to the PFGE pulsotype 2 was characterized. The results revealed that both strains are safe for human use, successfully survive the simulated gastrointestinal conditions, have potential to transiently colonize the gastrointestinal tract (GIT) and have a protective immunomodulatory effect, inducing the production of proinflammatory cytokine IL17 and regulatory cytokine IL10, while decreasing the production of proinflammatory cytokine IFN-gamma. In conclusion, the results of this study suggest that consumption of A. ursinum might have health-promoting properties, including anticancer effects, while L. fermentum strains isolated from A. ursinum leaves could be used as probiotics for human consumption.
PB  - Frontiers Media Sa, Lausanne
T2  - Frontiers in Microbiology
T1  - Antioxidant and Antiproliferative Activity of Allium ursinum and Their Associated Microbiota During Simulated in vitro Digestion in the Presence of Food Matrix
VL  - 11
DO  - 10.3389/fmicb.2020.601616
ER  - 

@article{
author = "Stanisavljević, Nemanja and Soković Bajić, Svetlana and Jovanović, Živko and Matić, Ivana and Tolinački, Maja and Popović, Dušanka and Popović, Nikola and Terzić-Vidojević, Amarela and Golić, Nataša and Beskoski, Vladimir and Samardžić, Jelena",
year = "2020",
abstract = "In this study, for the first time, the comprehensive analysis of antiproliferative and antioxidant activities of ramson, followed by the analysis of its associated microbiota and health-promoting effects of lactic acid bacteria (LAB), was performed. Ramson (Allium ursinum) is recognized as a medicinal plant with a long history of use in traditional medicine due to its antimicrobial and antioxidant activity. In this study the influence of in vitro gastrointestinal digestion on the cytotoxic activity of A. ursinum extracts against human malignant cell lines was demonstrated. Seven sulfur compounds, the degradation products of thiosulfinates, including diallyl disulfide were shown to inhibit proliferation of malignant cells by inducing accumulation within G2/M phase as well as to induce apoptosis through activation of caspase-3 and mitochondrial signaling pathway. Further, the A. ursinum microbiota, particularly LAB with potential probiotic effects, was analyzed by culture-dependent method and culture-independent method [denaturing gradient gel electrophoresis (DGGE)]. The obtained results revealed that the most abundant genera were Streptococcus, Lactobacillus, and Bacillus. The Lactobacillus genus was mainly represented by L. fermentum. The pulsed-field gel electrophoresis (PFGE) analysis revealed the presence of two PFGE pulsotypes. The probiotic potential of the strain L. fermentum BGSR163 belonging to PFGE pulsotype 1 and the strain L. fermentum BGSR227 belonging to the PFGE pulsotype 2 was characterized. The results revealed that both strains are safe for human use, successfully survive the simulated gastrointestinal conditions, have potential to transiently colonize the gastrointestinal tract (GIT) and have a protective immunomodulatory effect, inducing the production of proinflammatory cytokine IL17 and regulatory cytokine IL10, while decreasing the production of proinflammatory cytokine IFN-gamma. In conclusion, the results of this study suggest that consumption of A. ursinum might have health-promoting properties, including anticancer effects, while L. fermentum strains isolated from A. ursinum leaves could be used as probiotics for human consumption.",
publisher = "Frontiers Media Sa, Lausanne",
journal = "Frontiers in Microbiology",
title = "Antioxidant and Antiproliferative Activity of Allium ursinum and Their Associated Microbiota During Simulated in vitro Digestion in the Presence of Food Matrix",
volume = "11",
doi = "10.3389/fmicb.2020.601616"
}

Stanisavljević, N., Soković Bajić, S., Jovanović, Ž., Matić, I., Tolinački, M., Popović, D., Popović, N., Terzić-Vidojević, A., Golić, N., Beskoski, V.,& Samardžić, J.. (2020). Antioxidant and Antiproliferative Activity of Allium ursinum and Their Associated Microbiota During Simulated in vitro Digestion in the Presence of Food Matrix. in Frontiers in Microbiology
Frontiers Media Sa, Lausanne., 11.
https://doi.org/10.3389/fmicb.2020.601616

Stanisavljević N, Soković Bajić S, Jovanović Ž, Matić I, Tolinački M, Popović D, Popović N, Terzić-Vidojević A, Golić N, Beskoski V, Samardžić J. Antioxidant and Antiproliferative Activity of Allium ursinum and Their Associated Microbiota During Simulated in vitro Digestion in the Presence of Food Matrix. in Frontiers in Microbiology. 2020;11.
doi:10.3389/fmicb.2020.601616 .

Stanisavljević, Nemanja, Soković Bajić, Svetlana, Jovanović, Živko, Matić, Ivana, Tolinački, Maja, Popović, Dušanka, Popović, Nikola, Terzić-Vidojević, Amarela, Golić, Nataša, Beskoski, Vladimir, Samardžić, Jelena, "Antioxidant and Antiproliferative Activity of Allium ursinum and Their Associated Microbiota During Simulated in vitro Digestion in the Presence of Food Matrix" in Frontiers in Microbiology, 11 (2020),
https://doi.org/10.3389/fmicb.2020.601616 . .

TY  - JOUR
AU  - Bosnić, Dragana
AU  - Bosnić, Predrag
AU  - Nikolić, Dragana
AU  - Nikolić, Miroslav
AU  - Samardžić, Jelena
PY  - 2019
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1214
AB  - Copper (Cu) toxicity in plants may lead to iron (Fe), zinc (Zn) and manganese (Mn) deficiencies. Here, we investigated the effect of Si and Fe supply on the concentrations of micronutrients and metal-chelating amino acids nicotianamine (NA) and histidine (His) in leaves of cucumber plants exposed to Cu in excess. Cucumber (Cucumis sativus L.) was treated with 10 mu M Cu, and additional 100 mu M Fe or/and 1.5 mM Si for five days. High Cu and decreased Zn, Fe and Mn concentrations were found in Cu treatment. Additional Fe supply had a more pronounced effect in decreasing Cu accumulation and improving the molar ratio between micronutrients as compared to the Si supply. However, the simultaneous supply of Fe and Si was the most effective treatment in alleviation of Cu-induced deficiency of Fe, Zn and Mn. Additional Fe supply increased the His but not NA concentration, while Si supply significantly increased both NA and His whereby the NA:Cu and His:Cu molar ratios exceeded the control values indicating that Si recruits Cu-chelation to achieve Cu tolerance. In conclusion, Si-mediated alleviation of Cu toxicity was directed toward Cu tolerance while Fe-alleviative effect was due to a dramatic decrease in Cu accumulation.
PB  - MDPI, Basel
T2  - Plants-Basel
T1  - Silicon and Iron Differently Alleviate Copper Toxicity in Cucumber Leaves
IS  - 12
VL  - 8
DO  - 10.3390/plants8120554
ER  - 

@article{
author = "Bosnić, Dragana and Bosnić, Predrag and Nikolić, Dragana and Nikolić, Miroslav and Samardžić, Jelena",
year = "2019",
abstract = "Copper (Cu) toxicity in plants may lead to iron (Fe), zinc (Zn) and manganese (Mn) deficiencies. Here, we investigated the effect of Si and Fe supply on the concentrations of micronutrients and metal-chelating amino acids nicotianamine (NA) and histidine (His) in leaves of cucumber plants exposed to Cu in excess. Cucumber (Cucumis sativus L.) was treated with 10 mu M Cu, and additional 100 mu M Fe or/and 1.5 mM Si for five days. High Cu and decreased Zn, Fe and Mn concentrations were found in Cu treatment. Additional Fe supply had a more pronounced effect in decreasing Cu accumulation and improving the molar ratio between micronutrients as compared to the Si supply. However, the simultaneous supply of Fe and Si was the most effective treatment in alleviation of Cu-induced deficiency of Fe, Zn and Mn. Additional Fe supply increased the His but not NA concentration, while Si supply significantly increased both NA and His whereby the NA:Cu and His:Cu molar ratios exceeded the control values indicating that Si recruits Cu-chelation to achieve Cu tolerance. In conclusion, Si-mediated alleviation of Cu toxicity was directed toward Cu tolerance while Fe-alleviative effect was due to a dramatic decrease in Cu accumulation.",
publisher = "MDPI, Basel",
journal = "Plants-Basel",
title = "Silicon and Iron Differently Alleviate Copper Toxicity in Cucumber Leaves",
number = "12",
volume = "8",
doi = "10.3390/plants8120554"
}

Bosnić, D., Bosnić, P., Nikolić, D., Nikolić, M.,& Samardžić, J.. (2019). Silicon and Iron Differently Alleviate Copper Toxicity in Cucumber Leaves. in Plants-Basel
MDPI, Basel., 8(12).
https://doi.org/10.3390/plants8120554

Bosnić D, Bosnić P, Nikolić D, Nikolić M, Samardžić J. Silicon and Iron Differently Alleviate Copper Toxicity in Cucumber Leaves. in Plants-Basel. 2019;8(12).
doi:10.3390/plants8120554 .

Bosnić, Dragana, Bosnić, Predrag, Nikolić, Dragana, Nikolić, Miroslav, Samardžić, Jelena, "Silicon and Iron Differently Alleviate Copper Toxicity in Cucumber Leaves" in Plants-Basel, 8, no. 12 (2019),
https://doi.org/10.3390/plants8120554 . .

TY  - JOUR
AU  - Nikolić, Dragana
AU  - Nešić, Sofija
AU  - Bosnić, Dragana
AU  - Kostić, Ljiljana
AU  - Nikolić, Miroslav
AU  - Samardžić, Jelena
PY  - 2019
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1289
AB  - The beneficial effects of silicon (Si) have been shown on plants using reduction-based strategy for iron (Fe) acquisition. Here we investigated the influence of Si on Fe deficiency stress alleviation in barley (Hordeum vulgare), a crop plant which uses the chelation-based strategy for Fe acquisition. Analyses of chlorophyll content, ROS accumulation, antioxidative status, concentrations of Fe and other micronutrients, along with the expression of Strategy II genes were studied in response to Si supply. Si successfully ameliorated Fe deficiency in barley, diminishing chlorophyll and biomass loss, and improving the activity of antioxidative enzymes, resulting in lowered reactive oxidative species accumulation in the youngest leaves. Alleviation of Fe deficiency stress correlated well with the Si-induced increase of Fe content in the youngest leaves, while it was decreased in root. Moreover, Si nutrition lowered accumulation of other micronutrients in the youngest leaves of Fe deprived plants, by retaining them in the root. On the transcriptional level, Si led to an expedient increase in the expression of genes involved in Strategy II Fe acquisition in roots at the early stage of Fe deficiency stress, while decreasing their expression in a prolonged stress response. Expression of Strategy II genes was remarkably upregulated in the leaves of Si supplied plants. This study broadens the perspective of mechanisms of Si action, providing evidence for ameliorative effects of Si on Strategy II plants, including its influence on accumulation and distribution of microelements, as well as on the expression of the Strategy II genes.
PB  - Frontiers Media Sa, Lausanne
T2  - Frontiers in Plant Science
T1  - Silicon Alleviates Iron Deficiency in Barley by Enhancing Expression of Strategy II Genes and Metal Redistribution
VL  - 10
DO  - 10.3389/fpls.2019.00416
ER  - 

@article{
author = "Nikolić, Dragana and Nešić, Sofija and Bosnić, Dragana and Kostić, Ljiljana and Nikolić, Miroslav and Samardžić, Jelena",
year = "2019",
abstract = "The beneficial effects of silicon (Si) have been shown on plants using reduction-based strategy for iron (Fe) acquisition. Here we investigated the influence of Si on Fe deficiency stress alleviation in barley (Hordeum vulgare), a crop plant which uses the chelation-based strategy for Fe acquisition. Analyses of chlorophyll content, ROS accumulation, antioxidative status, concentrations of Fe and other micronutrients, along with the expression of Strategy II genes were studied in response to Si supply. Si successfully ameliorated Fe deficiency in barley, diminishing chlorophyll and biomass loss, and improving the activity of antioxidative enzymes, resulting in lowered reactive oxidative species accumulation in the youngest leaves. Alleviation of Fe deficiency stress correlated well with the Si-induced increase of Fe content in the youngest leaves, while it was decreased in root. Moreover, Si nutrition lowered accumulation of other micronutrients in the youngest leaves of Fe deprived plants, by retaining them in the root. On the transcriptional level, Si led to an expedient increase in the expression of genes involved in Strategy II Fe acquisition in roots at the early stage of Fe deficiency stress, while decreasing their expression in a prolonged stress response. Expression of Strategy II genes was remarkably upregulated in the leaves of Si supplied plants. This study broadens the perspective of mechanisms of Si action, providing evidence for ameliorative effects of Si on Strategy II plants, including its influence on accumulation and distribution of microelements, as well as on the expression of the Strategy II genes.",
publisher = "Frontiers Media Sa, Lausanne",
journal = "Frontiers in Plant Science",
title = "Silicon Alleviates Iron Deficiency in Barley by Enhancing Expression of Strategy II Genes and Metal Redistribution",
volume = "10",
doi = "10.3389/fpls.2019.00416"
}

Nikolić, D., Nešić, S., Bosnić, D., Kostić, L., Nikolić, M.,& Samardžić, J.. (2019). Silicon Alleviates Iron Deficiency in Barley by Enhancing Expression of Strategy II Genes and Metal Redistribution. in Frontiers in Plant Science
Frontiers Media Sa, Lausanne., 10.
https://doi.org/10.3389/fpls.2019.00416

Nikolić D, Nešić S, Bosnić D, Kostić L, Nikolić M, Samardžić J. Silicon Alleviates Iron Deficiency in Barley by Enhancing Expression of Strategy II Genes and Metal Redistribution. in Frontiers in Plant Science. 2019;10.
doi:10.3389/fpls.2019.00416 .

Nikolić, Dragana, Nešić, Sofija, Bosnić, Dragana, Kostić, Ljiljana, Nikolić, Miroslav, Samardžić, Jelena, "Silicon Alleviates Iron Deficiency in Barley by Enhancing Expression of Strategy II Genes and Metal Redistribution" in Frontiers in Plant Science, 10 (2019),
https://doi.org/10.3389/fpls.2019.00416 . .

TY  - JOUR
AU  - De Backer, G.
AU  - Jankowski, P.
AU  - Dilić, M.
AU  - Lalić, N.
AU  - Lović, D.
AU  - Miličić, D.
AU  - Vulić, D.
AU  - Begić, A.
AU  - Durak Nalbantić, A.
AU  - Hadzibegić, N.
AU  - Kapidjić, S.
AU  - Resić, N.
AU  - Sabanović Bajramović, N.
AU  - Zvizdić, F.
AU  - Kovacević-Preradović, T.
AU  - Popović-Pejicić, S.
AU  - Đekić, D.
AU  - Gnjatić, T.
AU  - Knezević, T.
AU  - Stanetić, B.
AU  - Topić, G.
AU  - Milicić, D.
AU  - Bosnić, A.
AU  - Dubravcić, M.
AU  - Pavasović, S.
AU  - Samardžić, Jelena
AU  - Batinić, T.
AU  - Delić-Brkljacić, D.
AU  - Golubić, K.
AU  - Kordić, K.
AU  - Nedić, M.
AU  - Olujić, D.
AU  - Sedinić, V.
AU  - Blazević, T.
AU  - Pasalić, A.
AU  - Percić, M.
AU  - Sikić, J.
AU  - Aleksić, M.
AU  - Đokić, Jelena
AU  - Hinić, S.
AU  - Zdravković, M.
AU  - Lalić, N.M.
AU  - Jotić, A.
AU  - Lalić, K.
AU  - Lukić, L.
AU  - Milicić, T.
AU  - Macesić, M.
AU  - Stanarcić Gajović, J.
AU  - Stoiljković, M.
AU  - Đorđević, D.
AU  - Kostić, S.
AU  - Tasić, I.
AU  - Vuković, A.
AU  - Kugonjič, U.
AU  - (broj koatora 519)
PY  - 2019
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1231
AB  - Background and aims: One of the objectives of the ESC-EORP EUROASPIRE V survey is to determine how well European guidelines on the management of dyslipidaemias are implemented in coronary patients. Methods: Standardized methods were used by trained technicians to collect information on 7824 patients from 130 centers in 27 countries, from the medical records and at a visit at least 6 months after hospitalization for a coronary event. All lipid measurements were performed in one central laboratory. Patients were divided into three groups: on high-intensity LDL-C-lowering-drug therapy (LLT), on low or moderate-intensity LLT and on no LLT. Results: At the time of the visit, almost half of the patients were on a high-intensity LLT. Between hospital discharge and the visit, LLT had been reduced in intensity or interrupted in 20.8% of the patients and had been started or increased in intensity in 11.7%. In those who had interrupted LLT or had reduced the intensity, intolerance to LLT and the advice of their physician were reported as the reason why in 15.8 and 36.8% of the cases, respectively. LDL-C control was better in those on a high-intensity LLT compared to those on low or moderate intensity LLT. LDL-C control was better in men than women and in patients with self-reported diabetes. Conclusions: The results of the EUROASPIRE V survey show that most coronary patients have a less than optimal management of LDL-C. More professional strategies are needed, aiming at lifestyle changes and LLT adapted to the need of the individual patient.
PB  - Elsevier Ireland Ltd
T2  - Atherosclerosis
T1  - Management of dyslipidaemia in patients with coronary heart disease: Results from the ESC-EORP EUROASPIRE V survey in 27 countries
EP  - 146
SP  - 135
VL  - 285
DO  - 10.1016/j.atherosclerosis.2019.03.014
ER  - 

@article{
author = "De Backer, G. and Jankowski, P. and Dilić, M. and Lalić, N. and Lović, D. and Miličić, D. and Vulić, D. and Begić, A. and Durak Nalbantić, A. and Hadzibegić, N. and Kapidjić, S. and Resić, N. and Sabanović Bajramović, N. and Zvizdić, F. and Kovacević-Preradović, T. and Popović-Pejicić, S. and Đekić, D. and Gnjatić, T. and Knezević, T. and Stanetić, B. and Topić, G. and Milicić, D. and Bosnić, A. and Dubravcić, M. and Pavasović, S. and Samardžić, Jelena and Batinić, T. and Delić-Brkljacić, D. and Golubić, K. and Kordić, K. and Nedić, M. and Olujić, D. and Sedinić, V. and Blazević, T. and Pasalić, A. and Percić, M. and Sikić, J. and Aleksić, M. and Đokić, Jelena and Hinić, S. and Zdravković, M. and Lalić, N.M. and Jotić, A. and Lalić, K. and Lukić, L. and Milicić, T. and Macesić, M. and Stanarcić Gajović, J. and Stoiljković, M. and Đorđević, D. and Kostić, S. and Tasić, I. and Vuković, A. and Kugonjič, U. and (broj koatora 519)",
year = "2019",
abstract = "Background and aims: One of the objectives of the ESC-EORP EUROASPIRE V survey is to determine how well European guidelines on the management of dyslipidaemias are implemented in coronary patients. Methods: Standardized methods were used by trained technicians to collect information on 7824 patients from 130 centers in 27 countries, from the medical records and at a visit at least 6 months after hospitalization for a coronary event. All lipid measurements were performed in one central laboratory. Patients were divided into three groups: on high-intensity LDL-C-lowering-drug therapy (LLT), on low or moderate-intensity LLT and on no LLT. Results: At the time of the visit, almost half of the patients were on a high-intensity LLT. Between hospital discharge and the visit, LLT had been reduced in intensity or interrupted in 20.8% of the patients and had been started or increased in intensity in 11.7%. In those who had interrupted LLT or had reduced the intensity, intolerance to LLT and the advice of their physician were reported as the reason why in 15.8 and 36.8% of the cases, respectively. LDL-C control was better in those on a high-intensity LLT compared to those on low or moderate intensity LLT. LDL-C control was better in men than women and in patients with self-reported diabetes. Conclusions: The results of the EUROASPIRE V survey show that most coronary patients have a less than optimal management of LDL-C. More professional strategies are needed, aiming at lifestyle changes and LLT adapted to the need of the individual patient.",
publisher = "Elsevier Ireland Ltd",
journal = "Atherosclerosis",
title = "Management of dyslipidaemia in patients with coronary heart disease: Results from the ESC-EORP EUROASPIRE V survey in 27 countries",
pages = "146-135",
volume = "285",
doi = "10.1016/j.atherosclerosis.2019.03.014"
}

De Backer, G., Jankowski, P., Dilić, M., Lalić, N., Lović, D., Miličić, D., Vulić, D., Begić, A., Durak Nalbantić, A., Hadzibegić, N., Kapidjić, S., Resić, N., Sabanović Bajramović, N., Zvizdić, F., Kovacević-Preradović, T., Popović-Pejicić, S., Đekić, D., Gnjatić, T., Knezević, T., Stanetić, B., Topić, G., Milicić, D., Bosnić, A., Dubravcić, M., Pavasović, S., Samardžić, J., Batinić, T., Delić-Brkljacić, D., Golubić, K., Kordić, K., Nedić, M., Olujić, D., Sedinić, V., Blazević, T., Pasalić, A., Percić, M., Sikić, J., Aleksić, M., Đokić, J., Hinić, S., Zdravković, M., Lalić, N.M., Jotić, A., Lalić, K., Lukić, L., Milicić, T., Macesić, M., Stanarcić Gajović, J., Stoiljković, M., Đorđević, D., Kostić, S., Tasić, I., Vuković, A., Kugonjič, U.,& (broj koatora 519). (2019). Management of dyslipidaemia in patients with coronary heart disease: Results from the ESC-EORP EUROASPIRE V survey in 27 countries. in Atherosclerosis
Elsevier Ireland Ltd., 285, 135-146.
https://doi.org/10.1016/j.atherosclerosis.2019.03.014

De Backer G, Jankowski P, Dilić M, Lalić N, Lović D, Miličić D, Vulić D, Begić A, Durak Nalbantić A, Hadzibegić N, Kapidjić S, Resić N, Sabanović Bajramović N, Zvizdić F, Kovacević-Preradović T, Popović-Pejicić S, Đekić D, Gnjatić T, Knezević T, Stanetić B, Topić G, Milicić D, Bosnić A, Dubravcić M, Pavasović S, Samardžić J, Batinić T, Delić-Brkljacić D, Golubić K, Kordić K, Nedić M, Olujić D, Sedinić V, Blazević T, Pasalić A, Percić M, Sikić J, Aleksić M, Đokić J, Hinić S, Zdravković M, Lalić N, Jotić A, Lalić K, Lukić L, Milicić T, Macesić M, Stanarcić Gajović J, Stoiljković M, Đorđević D, Kostić S, Tasić I, Vuković A, Kugonjič U, (broj koatora 519). Management of dyslipidaemia in patients with coronary heart disease: Results from the ESC-EORP EUROASPIRE V survey in 27 countries. in Atherosclerosis. 2019;285:135-146.
doi:10.1016/j.atherosclerosis.2019.03.014 .

De Backer, G., Jankowski, P., Dilić, M., Lalić, N., Lović, D., Miličić, D., Vulić, D., Begić, A., Durak Nalbantić, A., Hadzibegić, N., Kapidjić, S., Resić, N., Sabanović Bajramović, N., Zvizdić, F., Kovacević-Preradović, T., Popović-Pejicić, S., Đekić, D., Gnjatić, T., Knezević, T., Stanetić, B., Topić, G., Milicić, D., Bosnić, A., Dubravcić, M., Pavasović, S., Samardžić, Jelena, Batinić, T., Delić-Brkljacić, D., Golubić, K., Kordić, K., Nedić, M., Olujić, D., Sedinić, V., Blazević, T., Pasalić, A., Percić, M., Sikić, J., Aleksić, M., Đokić, Jelena, Hinić, S., Zdravković, M., Lalić, N.M., Jotić, A., Lalić, K., Lukić, L., Milicić, T., Macesić, M., Stanarcić Gajović, J., Stoiljković, M., Đorđević, D., Kostić, S., Tasić, I., Vuković, A., Kugonjič, U., (broj koatora 519), "Management of dyslipidaemia in patients with coronary heart disease: Results from the ESC-EORP EUROASPIRE V survey in 27 countries" in Atherosclerosis, 285 (2019):135-146,
https://doi.org/10.1016/j.atherosclerosis.2019.03.014 . .