1. TGA transcription factors : structural characteristics as basis for functional variabilityŠpela Tomaž, Kristina Gruden, Anna Coll Rius, 2022, review article Abstract: TGA transcription factors are essential regulators of various cellular processes, their activity connected to different hormonal pathways, interacting proteins and regulatory elements. Belonging to the basic region leucine zipper (bZIP) family, TGAs operate by binding to their target DNA sequence as dimers through a conserved bZIP domain. Despite sharing the core DNA-binding sequence, the TGA paralogues exert somewhat different DNA-binding preferences. Sequence variability of their N- and C-terminal protein parts indicates their importance in defining TGA functional specificity through interactions with diverse proteins, affecting their DNA-binding properties. In this review, we provide a short and concise summary on plant TGA transcription factors from a structural point of view, including the relation of their structural characteristics to their functional roles in transcription regulation.
Keywords: DOG1 domain, functional variability, intrinsically disordered regions, plant transcription regulation, post-translational modifications, structural characteristics, TGA transcription factors
Published in DiRROS: 05.08.2024; Views: 101; Downloads: 134
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2. Socioeconomic and environmental importance of the fish market and fisheries in SloveniaAlex Mavrič, Andreja Ramšak, Štefan Bojnec, 2021, original scientific article Abstract: The paper analyses the importance of fisheries and the fish market in Slovenia based on primary information obtained from interviews and secondary data obtained from various sources. The study focuses on the sustainability aspects of fisheries and the fish market in Slovenia, emphasizing socioeconomic factors, problems and anomalies in the market, ecological aspects, and other sustainable development factors as environmental protection and the implementation of sustainable development measures, as well as overfishing and ineffective fisheries management. Most of shortcomings are related to the traceability of fish in the value chain, misleading customers with false information, and price-quality deception. While these findings are country-specific, they have broader implications and highlight opportunities for improving the fisheries and fish market situation in Slovenia and the international trade of fish and fishery products.
Keywords: fisheries, aquaculture, sustainability, socioeconomic factors, fraud, value chain
Published in DiRROS: 01.08.2024; Views: 298; Downloads: 162
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3. Seasonal abundance, vertical distribution and life history traits of Mediterranean mud shrimp Upogebia pusilla (Decapoda: Gebiidea) on the Slovenian coastJure Jugovic, Eva Horvat, Lovrenc Lipej, 2017, original scientific article Abstract: We studied seasonal abundance, vertical distribution and life history traits of the Mediterranean
mud shrimp (Upogebia pusilla) in the mediolittoral zone in Slovenia. At two localities (Strunjan and
Lazaret), quantitative samples from three plots (1 m2
each) at (0 cm), below (-50 cm) and above
(+50 cm) mean water level were taken once every two months, in alternation. A set of parameters
was also recorded, including vegetation cover, sediment type, air and sea temperature, pH, salinity
and oxygen levels. Highest abundance was recorded during the warm period of the year, with peak
abundance in June 2012 (21 % of total sample). Lowest plots were always occupied with the highest
densities of mud shrimps. Males dominated during the winter while ovigerous females reached the
peak in June (>40 % of all animals). In June at least 2/3 of females were ovigerous. Estimated mean
incubation period was 31 days. We determined four periods in relation to the species’ reproductive
activity. Early reproductive period (April) was characterised by emergence of first ovigerous
females, while main reproductive period (May–July) was characterised by peak of reproduction.
In post-reproductive (August–October), and non-reproductive (November–March) periods, no
ovigerous females or newly hatched offspring were recorded.
Keywords: abiotic factors, abundance, spatial variation, temporal variation
Published in DiRROS: 25.07.2024; Views: 305; Downloads: 76
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4. Real-life long-term outcomes of upfront surgery in patients with resectable stage I-IIIA non-small cell lung cancerMarko Bitenc, Tanja Čufer, Izidor Kern, Martina Miklavčič, Sabrina Petrovič, Vida Groznik, Aleksander Sadikov, 2022, original scientific article Abstract: Treatment of early-stage non-small cell lung cancer (NSCLC) is rapidly evolving. When introducing novelties, real-life data on effectiveness of currently used treatment strategies are needed. The present study evaluated outcomes of stage I–IIIA NSCLC patients treated with upfront radical surgery in everyday clinical practice, between 2010–2017. Data of 539 consecutive patients were retrieved from a prospective hospital-based registry. All diagnostic, treatment and follow-up procedures were performed at the same thoracic oncology centre according to the valid guidelines. The primary outcome was overall survival (OS) analysed by clinical(c) and pathological(p) TNM (tumour, node, metastases) stage. The impact of clinicopathological characteristics on OS was evaluated using univariable (UVA) and multivariable regression analysis (MVA). With a median follow-up of 53.9 months, median OS and 5-year OS rate in the overall population were 90.4 months and 64.4%. Five-year OS rates by pTNM stage I, II and IIIA were 70.2%, 60.21%, and 49.9%, respectively. Both cTNM and pTNM stages were associated with OS; but only pTNM retained its independent prognostic value (p = 0.003) in MVA. Agreement between cTNM and pTNM was 69.0%. Next to pTNM, age (p = 0.001) and gender (p = 0.004) retained their independent prognostic value for OS. The study showed favourable outcomes of resectable stage I–IIIA NSCLC treated with upfront surgery in real-life. Relatively low agreement between cTNM and pTNM stages and independent prognostic value of only pTNM, observed in real-life data, suggest that surgery remains the most accurate provider of the anatomical stage of disease and important upfront therapy.
Keywords: resectable NSCLC, upfront surgery, real-life data, overall survival, prognostic factors
Published in DiRROS: 25.07.2024; Views: 135; Downloads: 107
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5. IGF2 and IGF1R identified as novel tip cell genes in primary microvascular endothelial cell monolayersMarchien G. Dallinga, Bahar Yetkin-Arik, Richelle P. Kayser, Ilse M.C. Vogels, Patrycja Nowak-Sliwinska, Arjan W. Griffioen, Cornelis J. F. van Noorden, Ingeborg Klaassen, Reinier O. Schlingemann, 2018, original scientific article Abstract: Tip cells, the leading cells of angiogenic sprouts, were identified in cultures of human umbilical vein endothelial cells (HUVECs) by using CD34 as a marker. Here, we show that tip cells are also present in primary human microvascular endothelial cells (hMVECs), a more relevant endothelial cell type for angiogenesis. By means of flow cytometry, immunocytochemistry, and qPCR, it is shown that endothelial cell cultures contain a dynamic population of CD34+ cells with many hallmarks of tip cells, including filopodia-like extensions, elevated mRNA levels of known tip cell genes, and responsiveness to stimulation with VEGF and inhibition by DLL4. Furthermore, we demonstrate that our in vitro tip cell model can be exploited to investigate cellular and molecular mechanisms in tip cells and to discover novel targets for anti-angiogenesis therapy in patients. Small interfering RNA (siRNA) was used to knockdown gene expression of the known tip cell genes angiopoietin 2 (ANGPT2) and tyrosine kinase with immunoglobulin-like and EGF-like domains 1 (TIE1), which resulted in similar effects on tip cells and sprouting as compared to inhibition of tip cells in vivo. Finally, we identified two novel tip cell-specific genes in CD34+ tip cells in vitro: insulin-like growth factor 2 (IGF2) and IGF-1-receptor (IGF1R). Knockdown of these genes resulted in a significant decrease in the fraction of tip cells and in the extent of sprouting in vitro and in vivo. In conclusion, this study shows that by using our in vitro tip cell model, two novel essential tip cells genes are identified.
Keywords: Angiogenesis, tip cells, CD34, IGF2, endothelial cells, cultured cells, endothelial growth factors
Published in DiRROS: 24.07.2024; Views: 137; Downloads: 120
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6. IGF-binding proteins 3 and 4 are regulators of sprouting angiogenesisMarchien G. Dallinga, Yasmin I. Habani, Richelle P. Kayser, Cornelis J. F. van Noorden, Ingeborg Klaassen, Reinier O. Schlingemann, 2020, original scientific article Abstract: Purpose
We have previously identified insulin-like growth factor 2 (IGF2) and insulin-like growth factor 1 receptor (IGF1R) as essential proteins for tip cell maintenance and sprouting angiogenesis. In this study, we aim to identify other IGF family members involved in endothelial sprouting angiogenesis.
Methods
Effects on sprouting were analyzed in human umbilical vein endothelial cells (HUVECs) using the spheroid-based sprouting model, and were quantified as mean number of sprouts per spheroid and average sprout length. RNA silencing technology was used to knockdown gene expression. Recombinant forms of the ligands (IGF1 and IGF2, insulin) and the IGF-binding proteins (IGFBP) 3 and 4 were used to induce excess effects. Effects on the tip cell phenotype were analyzed by measuring the fraction of CD34+ tip cells using flow cytometry and immunohistochemistry in a 3D angiogenesis model. Experiments were performed in the presence and absence of serum.
Results
Knockdown of IGF2 inhibited sprouting in HUVECs, in particular when cultured in the absence of serum, suggesting that components in serum influence the signaling of IGF2 in angiogenesis in vitro. We then determined the effects of IGFBP3 and IGFBP4, which are both present in serum, on IGF2-IGF1R signaling in sprouting angiogenesis in the absence of serum: knockdown of IGFBP3 significantly reduced sprouting angiogenesis, whereas knockdown of IGFBP4 resulted in increased sprouting angiogenesis in both flow cytometry analysis and immunohistochemical analysis of the 3D angiogenesis model. Other IGF family members except INSR did not affect IGF2-IGF1R signaling.
Conclusions
Serum components and IGF binding proteins regulate IGF2 effects on sprouting angiogenesis. Whereas IGFBP3 acts as co-factor for IGF2-IGF1R binding, IGFBP4 inhibits IGF2 signaling.
Keywords: Angiogenesis, tip cells, IGF2, IGF binding proteins, endothelial cells, cultured cells, endothelial growth factors
Published in DiRROS: 23.07.2024; Views: 112; Downloads: 131
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7. Diversity of molluscan assemblage in relation to biotic and abiotic variables in brown algal forestsMartina Orlando-Bonaca, Domen Trkov, Katja Klun, Valentina Pitacco, 2022, original scientific article Abstract: Canopy-forming macroalgae, mainly those belonging to the order Fucales, form the so-called brown algal forests, which are among the most productive assemblages in shallow coastal zones. Their vertical, branching canopies increase nearshore primary production, provide nursery areas for juvenile fish, and sustain understory assemblages of smaller algae and both sessile and vagile fauna. The majority of benthic invertebrates inhabiting these forests have larval stages that spend some time floating freely or swimming in the plankton. Therefore, canopy-forming macroalgae play an important role as species collectors related to larval supply and hydrodynamic processes. During the past several decades, brown algal forests have significantly reduced their extension and coverage in the Mediterranean basin, due to multiple interacting natural and anthropogenic pressures, with negative consequences also for the related fauna. The aim of this research was to examine how differences in macrophyte abundance and structure, as well as environmental variables, affect the associated molluscan communities in the shallow northern Adriatic Sea. Sampling sites with well-developed vegetation cover dominated by different canopy-forming species were selected in the shallow infralittoral belt of the northern Adriatic Sea in the spring–summer period of the years 2019 and 2020. Our results confirm the importance of algal forests for molluscan assemblage, with a total of 68 taxa of molluscs found associated with macrophytes. Gastropods showed the highest richness and abundance, followed by bivalves. Mollusc richness and diversity (in terms of biotic indices) were not related with the degree of development of canopy-forming species (in terms of total cover and total volume), nor with the ecological status of benthic macroalgae at different depths. On the contrary, the variability in molluscan taxa abundances was explained by some environmental variables, such as temperature, pH, light, and nitrates concentration.
Keywords: canopy-forming algae, coverage, molluscan assemblage, diversity, abiotic factors, Adriatic Sea
Published in DiRROS: 17.07.2024; Views: 104; Downloads: 135
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8. Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by subgroup 2 R2R3-MYBs in grapevineLuis Orduña, Miaomiao Li, David Navarro-Payá, Chen Zhang, A. Santiago, Pablo Romero, Živa Ramšak, Gabriele Magon, Janine Höll, Patrick Merz, Kristina Gruden, Alessandro Vannozzi, Dario Cantu, Jochen Bogs, Darren C. J. Wong, Shao-shan Carol Huang, José Tomás Matus, 2022, original scientific article Abstract: The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.
Keywords: secondary metabolism, regulatory networks, transcription factors, transcriptional regulation, DNA affinity purification sequencing
Published in DiRROS: 16.07.2024; Views: 120; Downloads: 122
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9. Breast cancer risk based on adapted IBIS prediction model in Slovenian women aged 40-49 years : coul it be better?Tjaša Oblak, Vesna Zadnik, Mateja Krajc, Katarina Lokar, Janez Žgajnar, 2020, original scientific article Keywords: breast surgery, IBIS, prediction models, risk factors
Published in DiRROS: 12.07.2024; Views: 124; Downloads: 58
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