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Article ; Online: Strategic concept paper for Bioeconomy in Slovenia: from a patchwork of good practices to an integrated, sustainable and robust bioeconomy system.

Juvančič, Luka / Berne, Sabina / Oven, Primož / Osojnik Črnivec, Ilja Gasan

Open research Europe

2023 Volume 3, Page(s) 167

Abstract: While Slovenia has significant bioeconomy potential, it remains underutilized, facing challenges in primary bioeconomy sectors, their integration along value chains, uptake of industrial innovation, and institutional coordination. This paper aims to ... ...

Abstract	While Slovenia has significant bioeconomy potential, it remains underutilized, facing challenges in primary bioeconomy sectors, their integration along value chains, uptake of industrial innovation, and institutional coordination. This paper aims to support the unlocking of Slovenia's bioeconomy potential, and foster sustainable and integrated development of its value chains. It provides the evidence base of the composition, volumes and current utilization of the available biomass streams from agriculture, forestry and aquatic systems. It discusses the potential uses of these resources and highlights the need for improved logistics and scalability. Additionally, the structure and performance of bioeconomy-related industries in Slovenia are examined, emphasizing the importance of firm consolidation and integration for successful bioeconomy development. It emphasizes the importance of sector-specific transformation pathways, from primary production to expanding hybrid sectors. The exchange between policymakers and stakeholders is encouraged to recognize synergies, accelerate cooperation, and improve economic performance while closing material and energy loops. The document also reviews the supporting environment for bioeconomy development and proposes steps for improved coordination and strategic planning.
Language	English
Publishing date	2023-10-03
Publishing country	Belgium
Document type	Journal Article
ISSN	2732-5121
ISSN (online)	2732-5121
DOI	10.12688/openreseurope.16181.1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Late Blight Resistance Conferred by

Blatnik, Eva / Horvat, Marinka / Berne, Sabina / Humar, Miha / Dolničar, Peter / Meglič, Vladimir

Plants (Basel, Switzerland)

2022 Volume 11, Issue 10

Abstract: Potato production worldwide is threatened by late blight, caused by the ... ...

Abstract	Potato production worldwide is threatened by late blight, caused by the oomycete
Language	English
Publishing date	2022-05-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants11101319
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Article: Hop Polyphenols in Relation to Verticillium Wilt Resistance and Their Antifungal Activity.

Berne, Sabina / Kovačević, Nataša / Kastelec, Damijana / Javornik, Branka / Radišek, Sebastjan

Plants (Basel, Switzerland)

2020 Volume 9, Issue 10

Abstract: 1) Background: Verticillium wilt (VW) of hop is a devastating disease caused by the soil-borne ... ...

Abstract	(1) Background: Verticillium wilt (VW) of hop is a devastating disease caused by the soil-borne fungi
Language	English
Publishing date	2020-10-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants9101318
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Article: Hop Polyphenols in Relation to Verticillium Wilt Resistance and Their Antifungal Activity

Berne, Sabina / Kovačević, Nataša / Kastelec, Damijana / Javornik, Branka / Radišek, Sebastjan

Plants. 2020 Oct. 06, v. 9, no. 10

2020

Abstract: 1) Background: Verticillium wilt (VW) of hop is a devastating disease caused by the soil-borne fungi Verticillium nonalfalfae and Verticillium dahliae. As suggested by quantitative trait locus (QTL) mapping and RNA-Seq analyses, the underlying molecular ...

Abstract	(1) Background: Verticillium wilt (VW) of hop is a devastating disease caused by the soil-borne fungi Verticillium nonalfalfae and Verticillium dahliae. As suggested by quantitative trait locus (QTL) mapping and RNA-Seq analyses, the underlying molecular mechanisms of resistance in hop are complex, consisting of preformed and induced defense responses, including the synthesis of various phenolic compounds. (2) Methods: We determined the total polyphenolic content at two phenological stages in roots and stems of 14 hop varieties differing in VW resistance, examined the changes in the total polyphenols of VW resistant variety Wye Target (WT) and susceptible Celeia (CE) on infection with V. nonalfalfae, and assessed the antifungal activity of six commercial phenolic compounds and total polyphenolic extracts from roots and stems of VW resistant WT and susceptible CE on the growth of two different V. nonalfalfae hop pathotypes. (3) Results: Generally, total polyphenols were higher in roots than stems and increased with maturation of the hop. Before flowering, the majority of VW resistant varieties had a significantly higher content of total polyphenols in stems than susceptible varieties. At the symptomatic stage of VW disease, total polyphenols decreased in VW resistant WT and susceptible CE plants in both roots and stems. The antifungal activity of total polyphenolic extracts against V. nonalfalfae was higher in hop extracts from stems than those from roots. Among the tested phenolic compounds, only p-coumaric acid and tyrosol markedly restricted fungal growth. (4) Conclusions: Although the correlation between VW resistance and total polyphenols content is not straightforward, higher levels of total polyphenols in the stems of the majority of VW resistant hop varieties at early phenological stages probably contribute to fast and efficient activation of signaling pathways, leading to successful defense against V. nonalfalfae infection.
Keywords	Verticillium dahliae ; Verticillium wilt ; antifungal properties ; flowering ; fungal growth ; p-coumaric acid ; pathotypes ; phenology ; polyphenols ; quantitative trait loci ; roots ; sequence analysis ; signal transduction ; soil fungi ; stems
Language	English
Dates of publication	2020-1006
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants9101318
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion.

Marton, Kristina / Flajšman, Marko / Radišek, Sebastjan / Košmelj, Katarina / Jakše, Jernej / Javornik, Branka / Berne, Sabina

PloS one

2018 Volume 13, Issue 6, Page(s) e0198971

Abstract: The vascular plant pathogen Verticillium nonalfalfae causes Verticillium wilt in several important crops. VnaSSP4.2 was recently discovered as a V. nonalfalfae virulence effector protein in the xylem sap of infected hop. Here, we expanded our search for ... ...

Abstract	The vascular plant pathogen Verticillium nonalfalfae causes Verticillium wilt in several important crops. VnaSSP4.2 was recently discovered as a V. nonalfalfae virulence effector protein in the xylem sap of infected hop. Here, we expanded our search for candidate secreted effector proteins (CSEPs) in the V. nonalfalfae predicted secretome using a bioinformatic pipeline built on V. nonalfalfae genome data, RNA-Seq and proteomic studies of the interaction with hop. The secretome, rich in carbohydrate active enzymes, proteases, redox proteins and proteins involved in secondary metabolism, cellular processing and signaling, includes 263 CSEPs. Several homologs of known fungal effectors (LysM, NLPs, Hce2, Cerato-platanins, Cyanovirin-N lectins, hydrophobins and CFEM domain containing proteins) and avirulence determinants in the PHI database (Avr-Pita1 and MgSM1) were found. The majority of CSEPs were non-annotated and were narrowed down to 44 top priority candidates based on their likelihood of being effectors. These were examined by spatio-temporal gene expression profiling of infected hop. Among the highest in planta expressed CSEPs, five deletion mutants were tested in pathogenicity assays. A deletion mutant of VnaUn.279, a lethal pathotype specific gene with sequence similarity to SAM-dependent methyltransferase (LaeA), had lower infectivity and showed highly reduced virulence, but no changes in morphology, fungal growth or conidiation were observed. Several putative secreted effector proteins that probably contribute to V. nonalfalfae colonization of hop were identified in this study. Among them, LaeA gene homolog was found to act as a potential novel virulence effector of V. nonalfalfae. The combined results will serve for future characterization of V. nonalfalfae effectors, which will advance our understanding of Verticillium wilt disease.
MeSH term(s)	Computer Simulation ; Fungal Proteins/metabolism ; Gene Expression Regulation, Fungal ; Humulus/metabolism ; Humulus/microbiology ; Plant Diseases/microbiology ; Proteome/metabolism ; Verticillium/metabolism ; Verticillium/pathogenicity ; Xylem/metabolism ; Xylem/microbiology
Chemical Substances	Fungal Proteins ; Proteome
Language	English
Publishing date	2018-06-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0198971
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2.

Xiao, Shenghua / Hu, Qin / Zhang, Xiaojun / Si, Huan / Liu, Shiming / Chen, Lin / Chen, Kun / Berne, Sabina / Yuan, Daojun / Lindsey, Keith / Zhang, Xianlong / Zhu, Longfu

Journal of experimental botany

2021 Volume 72, Issue 13, Page(s) 4721–4743

Abstract: Salicylic acid (SA) and brassinosteroids (BRs) are well known to regulate diverse processes of plant development and stress responses, but the mechanisms by which these phytohormones mediate the growth and defense trade-off are largely unclear. In ... ...

Abstract	Salicylic acid (SA) and brassinosteroids (BRs) are well known to regulate diverse processes of plant development and stress responses, but the mechanisms by which these phytohormones mediate the growth and defense trade-off are largely unclear. In addition, little is known about the roles of DEHYDRATION RESPONSIVE ELEMENT BINDING transcription factors, especially in biotic stress and plant growth. Here, we identified a cotton (Gossypium hirsutum) APETALA2/ETHYLENE RESPONSIVE FACTOR gene GhTINY2 that is strongly induced by Verticillium dahliae. Overexpression of GhTINY2 in cotton and Arabidopsis enhanced tolerance to V. dahliae, while knockdown of expression increased the susceptibility of cotton to the pathogen. GhTINY2 was found to promote SA accumulation and SA signaling transduction by directly activating expression of WRKY51. Moreover, GhTINY2-overexpressing cotton and Arabidopsis showed retardation of growth, increased sensitivity to inhibitors of BR biosynthesis, down-regulation of several BR-induced genes, and up-regulation of BR-repressed genes, while GhTINY2-RNAi cotton showed the opposite effects. We further determined that GhTINY2 negatively regulates BR signaling by interacting with BRASSINAZOLE-RESISTANT 1 (BZR1) and restraining its transcriptional activation of the expression of INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19). These findings indicate that GhTINY2 fine-tunes the trade-off between immunity and growth via indirect crosstalk between WRKY51-mediated SA biosynthesis and BZR1-IAA19-regulated BR signaling.
MeSH term(s)	Ascomycota ; Disease Resistance ; Gene Expression Regulation, Plant ; Gossypium/genetics ; Gossypium/metabolism ; Plant Development ; Plant Diseases ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Salicylic Acid ; Transcription Factors/genetics ; Verticillium
Chemical Substances	Plant Proteins ; Transcription Factors ; Salicylic Acid (O414PZ4LPZ)
Language	English
Publishing date	2021-01-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erab186
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Article ; Online: Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion.

Kristina Marton / Marko Flajšman / Sebastjan Radišek / Katarina Košmelj / Jernej Jakše / Branka Javornik / Sabina Berne

PLoS ONE, Vol 13, Iss 6, p e

2018 Volume 0198971

Abstract	The vascular plant pathogen Verticillium nonalfalfae causes Verticillium wilt in several important crops. VnaSSP4.2 was recently discovered as a V. nonalfalfae virulence effector protein in the xylem sap of infected hop. Here, we expanded our search for candidate secreted effector proteins (CSEPs) in the V. nonalfalfae predicted secretome using a bioinformatic pipeline built on V. nonalfalfae genome data, RNA-Seq and proteomic studies of the interaction with hop. The secretome, rich in carbohydrate active enzymes, proteases, redox proteins and proteins involved in secondary metabolism, cellular processing and signaling, includes 263 CSEPs. Several homologs of known fungal effectors (LysM, NLPs, Hce2, Cerato-platanins, Cyanovirin-N lectins, hydrophobins and CFEM domain containing proteins) and avirulence determinants in the PHI database (Avr-Pita1 and MgSM1) were found. The majority of CSEPs were non-annotated and were narrowed down to 44 top priority candidates based on their likelihood of being effectors. These were examined by spatio-temporal gene expression profiling of infected hop. Among the highest in planta expressed CSEPs, five deletion mutants were tested in pathogenicity assays. A deletion mutant of VnaUn.279, a lethal pathotype specific gene with sequence similarity to SAM-dependent methyltransferase (LaeA), had lower infectivity and showed highly reduced virulence, but no changes in morphology, fungal growth or conidiation were observed. Several putative secreted effector proteins that probably contribute to V. nonalfalfae colonization of hop were identified in this study. Among them, LaeA gene homolog was found to act as a potential novel virulence effector of V. nonalfalfae. The combined results will serve for future characterization of V. nonalfalfae effectors, which will advance our understanding of Verticillium wilt disease.
Keywords	Medicine ; R ; Science ; Q
Subject code	580 ; 572
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Comparative transcriptional analysis of hop responses to infection with Verticillium nonalfalfae.

Progar, Vasja / Jakše, Jernej / Štajner, Nataša / Radišek, Sebastjan / Javornik, Branka / Berne, Sabina

Plant cell reports

2017 Volume 36, Issue 10, Page(s) 1599–1613

Abstract: Key message: Dynamic transcriptome profiling revealed excessive, yet ineffective, immune response to V. nonalfalfae infection in susceptible hop, global gene downregulation in shoots of resistant hop and only a few infection-associated genes in roots. ... ...

Abstract	Key message: Dynamic transcriptome profiling revealed excessive, yet ineffective, immune response to V. nonalfalfae infection in susceptible hop, global gene downregulation in shoots of resistant hop and only a few infection-associated genes in roots. Hop (Humulus lupulus L.) production is hampered by Verticillium wilt, a disease predominantly caused by the soil-borne fungus Verticillium nonalfalfae. Only a few hop cultivars exhibit resistance towards it and mechanisms of this resistance have not been discovered. In this study, we compared global transcriptional responses in roots and shoots of resistant and susceptible hop plants infected by a lethal strain of V. nonalfalfae. Time-series differential gene expression profiles between infected and mock inoculated plants were determined and subjected to network-based analysis of functional enrichment. In the resistant hop cultivar, a remarkably low number of genes were differentially expressed in roots in response to V. nonalfalfae infection, while the majority of differentially expressed genes were down-regulated in shoots. The most significantly affected genes were related to cutin biosynthesis, cell wall biogenesis, lateral root development and terpenoid biosynthesis. On the other hand, susceptible hop exhibited a strong defence response in shoots and roots, including increased expression of genes associated with plant responses, such as innate immunity, wounding, jasmonic acid pathway and chitinase activity. Strong induction of defence-associated genes in susceptible hop and a low number of infection-responsive genes in the roots of resistant hop are consistent with previous findings, confirming the pattern of excessive response of the susceptible cultivar, which ultimately fails to protect the plant from V. nonalfalfae. This research offers a multifaceted overview of transcriptional responses of susceptible and resistant hop cultivars to V. nonalfalfae infection and represents a valuable resource in the study of this plant-pathogen interaction.
MeSH term(s)	Cannabaceae/genetics ; Cannabaceae/microbiology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant/genetics ; Host-Pathogen Interactions ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Plant Roots/genetics ; Plant Roots/microbiology ; Plant Shoots/genetics ; Plant Shoots/microbiology ; Verticillium/physiology
Language	English
Publishing date	2017-07-11
Publishing country	Germany
Document type	Comparative Study ; Journal Article
ZDB-ID	8397-5
ISSN	1432-203X ; 0721-085X ; 0721-7714
ISSN (online)	1432-203X
ISSN	0721-085X ; 0721-7714
DOI	10.1007/s00299-017-2177-1
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Article ; Online: APS8 Delays Tumor Growth in Mice by Inducing Apoptosis of Lung Adenocarcinoma Cells Expressing High Number of α7 Nicotinic Receptors.

Berne, Sabina / Čemažar, Maja / Frangež, Robert / Juntes, Polona / Kranjc, Simona / Grandič, Marjana / Savarin, Monika / Turk, Tom

Marine drugs

2018 Volume 16, Issue 10

Abstract: The alkylpyridinium polymer APS8, a potent antagonist of α7 nicotinic acetylcholine receptors (nAChRs), selectively induces apoptosis in non-small cell lung cancer cells but not in normal lung fibroblasts. To explore the potential therapeutic value of ... ...

Abstract	The alkylpyridinium polymer APS8, a potent antagonist of α7 nicotinic acetylcholine receptors (nAChRs), selectively induces apoptosis in non-small cell lung cancer cells but not in normal lung fibroblasts. To explore the potential therapeutic value of APS8 for at least certain types of lung cancer, we determined its systemic and organ-specific toxicity in mice, evaluated its antitumor activity against adenocarcinoma xenograft models, and examined the
MeSH term(s)	A549 Cells ; Adenocarcinoma of Lung/drug therapy ; Adenocarcinoma of Lung/metabolism ; Animals ; Apoptosis/drug effects ; Carcinoma, Non-Small-Cell Lung/metabolism ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Lung Neoplasms/drug therapy ; Lung Neoplasms/metabolism ; Mice ; Polymers/pharmacology ; Pyridinium Compounds/pharmacology ; RNA, Small Interfering/metabolism ; alpha7 Nicotinic Acetylcholine Receptor/metabolism
Chemical Substances	Polymers ; Pyridinium Compounds ; RNA, Small Interfering ; alpha7 Nicotinic Acetylcholine Receptor
Language	English
Publishing date	2018-10-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2175190-0
ISSN	1660-3397 ; 1660-3397
ISSN (online)	1660-3397
ISSN	1660-3397
DOI	10.3390/md16100367
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Article: Chitin-Binding Protein of

Volk, Helena / Marton, Kristina / Flajšman, Marko / Radišek, Sebastjan / Tian, Hui / Hein, Ingo / Podlipnik, Črtomir / Thomma, Bart P H J / Košmelj, Katarina / Javornik, Branka / Berne, Sabina

Molecular plant-microbe interactions : MPMI

2019 Volume 32, Issue 10, Page(s) 1378–1390

Abstract: During fungal infections, plant cells secrete chitinases, which digest chitin in the fungal cell walls. The recognition of released chitin oligomers via lysin motif (LysM)-containing immune host receptors results in the activation of defense signaling ... ...

Abstract	During fungal infections, plant cells secrete chitinases, which digest chitin in the fungal cell walls. The recognition of released chitin oligomers via lysin motif (LysM)-containing immune host receptors results in the activation of defense signaling pathways. We report here that
MeSH term(s)	Carrier Proteins ; Chitin/metabolism ; Chitinases ; Fungal Proteins/metabolism ; Molecular Docking Simulation ; Plant Diseases/microbiology ; Plants/enzymology ; Plants/immunology ; Verticillium
Chemical Substances	Carrier Proteins ; Fungal Proteins ; Chitin (1398-61-4) ; Chitinases (EC 3.2.1.14)
Language	English
Publishing date	2019-08-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-03-19-0079-R
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