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1.
Morfološka variabilnost črnike (Quercus ilex L.) v Sloveniji
Martin Jež, Robert Brus, Kristjan Jarni, 2024, izvirni znanstveni članek

Povzetek: V članku je predstavljena črnika (Quercus ilex L.), ena glavnih drevesnih vrst evmediteranske flore na območju Slovenije, kjer raste na razpršenih nahajališčih na severni meji svojega naravnega areala. Glavni namen raziskave je bil preučiti morfološko variabilnost njenih listov. V raziskavo je bilo vključenih sedem naravnih populacij črnike v Sloveniji. Morfometrijska analiza je pokazala veliko variabilnost listov in značilne razlike med populacijami, ki smo jih potrdili pri skoraj vseh preučevanih morfoloških znakih. Na podlagi ugotovljenih morfoloških razlik lahko slovenske populacije razdelimo v tri geografskomorfološke skupine: i) populacije na Goriškem (Sabotin, Sv. Gora in Lijak), ii) Nanos - Osp in iii) populaciji v dolini reke Dragonje. Morfološka variabilnost kot odsev genetske variabilnosti je posledica prilagoditve na lokalne okoljske razmere. Črnika v Sloveniji za zdaj ni ogrožena vrsta, vendar bi bilo pri morebitnih aktivnih varstvenih ukrepih za njeno ohranjanje smiselno čimbolj upoštevati ugotovljene tri geografsko-morfološke skupine.
Ključne besede: črnika, Quercus ilex, morfološka variabilnost, Slovenija, drevesni listi
Objavljeno v DiRROS: 12.09.2024; Ogledov: 173; Prenosov: 589
.pdf Celotno besedilo (1,50 MB)

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Cyanobacterial cyclic peptides can disrupt cytoskeleton organization in human astrocytes : a contribution to the understanding of the systemic toxicity of cyanotoxins
Anja Bubik, Robert Frangež, Monika C. Žužek, Ion Gutiérrez-Aguirre, Tamara Lah Turnšek, Bojan Sedmak, 2024, izvirni znanstveni članek

Povzetek: The systemic toxicity of cyclic peptides produced by cyanobacteria (CCPs) is not yet completely understood. Apart from the most known damages to the liver and kidneys, symptoms of their neurotoxicity have also been reported. Hepatotoxic CCPs, like microcystins, as well as non-hepatotoxic anabaenopeptins and planktopeptins, all exhibit cytotoxic and cytostatic effects on mammalian cells. However, responses of different cell types to CCPs depend on their specific modes of interaction with cell membranes. This study demonstrates that non-hepatotoxic planktopeptin BL1125 and anabaenopeptins B and F, at concentrations up to 10 µM, affect normal and tumor human astrocytes (NHA and U87-GM) in vitro by their almost immediate insertion into the lipid monolayer. Like microcystin-LR (up to 1 µM), they inhibit Ser/Thr phosphatases and reorganize cytoskeletal elements, with modest effects on their gene expression. Based on the observed effects on intermediate filaments and intermediate filament linkage elements, their direct or indirect influence on tubulin cytoskeletons via post-translational modifications, we conclude that the basic mechanism of CCP toxicities is the induction of inter- and intracellular communication failure. The assessed inhibitory activity on Ser/Thr phosphatases is also crucial since the signal transduction cascades are modulated by phosphorylation/dephosphorylation processes.
Ključne besede: astrocytes, cyclic cyanobacterial peptides, cytoskeletal organization, Ser/Thr phosphatases, systemic toxicity, cyanobacteria
Objavljeno v DiRROS: 28.08.2024; Ogledov: 192; Prenosov: 269
.pdf Celotno besedilo (21,09 MB)
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On the occurrence of early life stage of the king of herrings, Regalectus glesne (Actinopterygii: Lampriformes: Regalectidae), in the Adriatic Sea
Branko Dragičević, Armin Pallaoro, Robert Grgičević, Lovrenc Lipej, Jakov Dulčić, 2011, drugi znanstveni članki

Povzetek: The occurrence of an early life stage of the king of herrings, Regalecus glesne Ascanius, 1772, is reported for the first time from the Adriatic waters. A single larva (SL = 103.4 mm) was found alive in the waters of open Adriatic near a remote Island PalagruĹľa. Findings of early life stages of this species are very rare in the Mediterranean and have previously been reported only from the waters of the Strait of Sicily and Elba Island.
Ključne besede: fishes, ichthyology, Adriatic sea, Regalectidae, Regalectus glesne, oar fish, Adriatic Sea, larva, diversity, early life stage, record, king of herrings, Central Adriatic
Objavljeno v DiRROS: 07.08.2024; Ogledov: 168; Prenosov: 193
.pdf Celotno besedilo (1,87 MB)
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First substantiated record of a lessepsian migrant - the dusky spinefood, Siganus luridus (Actinopterzgii: Perciformes: Siganidae), in the Adriatic Sea
Jakov Dulčić, Branko Dragičević, Robert Grgičević, Lovrenc Lipej, 2011, drugi znanstveni članki

Povzetek: One specimen of the dusky spinefoot, Siganus luridus (Rüppell, 1829) (+, total length = 17.3 cm, total weight = 87.61 g), a lessepsian migrant, was captured in the Mljet Channel (Southern Adriatic, Croatian coast) on 15 November 2010. This is the second record of this species from the Adriatic, but first well documented and based on the captured specimen. First record occurred earlier in the Northern Adriatic, but was based solely on underwater observations.
Ključne besede: fishes, ichthyology, Adriatic sea, Siganidae, lessepsian migrants, diversity, origins, Mediterranean, new record, Adriatic Sea
Objavljeno v DiRROS: 07.08.2024; Ogledov: 202; Prenosov: 99
.pdf Celotno besedilo (1017,40 KB)
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SACE_5599, a putative regulatory protein, is involved in morphological differentiation and erythromycin production in Saccharopolyspora erythraea
Benjamin Kirm, Vasilka Magdevska, Miha Tome, Marinka Horvat, Katarina Karničar, Marko Petek, Robert Vidmar, Špela Baebler, Polona Jamnik, Štefan Fujs, Jaka Horvat, Marko Fonović, Boris Turk, Kristina Gruden, Hrvoje Petković, Gregor Kosec, 2013, izvirni znanstveni članek

Povzetek: Background Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. Genes encoding erythromycin biosynthesis are organized in a gene cluster, spanning over 60 kbp of DNA. Most often, gene clusters encoding biosynthesis of secondary metabolites contain regulatory genes. In contrast, the erythromycin gene cluster does not contain regulatory genes and regulation of its biosynthesis has therefore remained poorly understood, which has for a long time limited genetic engineering approaches for erythromycin yield improvement. Results We used a comparative proteomic approach to screen for potential regulatory proteins involved in erythromycin biosynthesis. We have identified a putative regulatory protein SACE_5599 which shows significantly higher levels of expression in an erythromycin high-producing strain, compared to the wild type S. erythraea strain. SACE_5599 is a member of an uncharacterized family of putative regulatory genes, located in several actinomycete biosynthetic gene clusters. Importantly, increased expression of SACE_5599 was observed in the complex fermentation medium and at controlled bioprocess conditions, simulating a high-yield industrial fermentation process in the bioreactor. Inactivation of SACE_5599 in the high-producing strain significantly reduced erythromycin yield, in addition to drastically decreasing sporulation intensity of the SACE_5599-inactivated strains when cultivated on ABSM4 agar medium. In contrast, constitutive overexpression of SACE_5599 in the wild type NRRL23338 strain resulted in an increase of erythromycin yield by 32%. Similar yield increase was also observed when we overexpressed the bldD gene, a previously identified regulator of erythromycin biosynthesis, thereby for the first time revealing its potential for improving erythromycin biosynthesis. Conclusions SACE_5599 is the second putative regulatory gene to be identified in S. erythraea which has positive influence on erythromycin yield. Like bldD, SACE_5599 is involved in morphological development of S. erythraea, suggesting a very close relationship between secondary metabolite biosynthesis and morphological differentiation in this organism. While the mode of action of SACE_5599 remains to be elucidated, the manipulation of this gene clearly shows potential for improvement of erythromycin production in S. erythraea in industrial setting. We have also demonstrated the applicability of the comparative proteomics approach for identifying new regulatory elements involved in biosynthesis of secondary metabolites in industrial conditions.
Ključne besede: erythromycin, polyketide, regulator, SACE_5599, lmbU, differentiation (biology), sporulation, strain improvement, metabolic engineering
Objavljeno v DiRROS: 02.08.2024; Ogledov: 184; Prenosov: 200
.pdf Celotno besedilo (1,18 MB)
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Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea
Katarina Karničar, Igor Drobnak, Marko Petek, Vasilka Magdevska, Jaka Horvat, Robert Vidmar, Špela Baebler, Ana Rotter, Polona Jamnik, Štefan Fujs, Boris Turk, Marko Fonović, Kristina Gruden, Gregor Kosec, Hrvoje Petković, 2016, izvirni znanstveni članek

Povzetek: Background Omics approaches have significantly increased our understanding of biological systems. However, they have had limited success in explaining the dramatically increased productivity of commercially important natural products by industrial high-producing strains, such as the erythromycin-producing actinomycete Saccharopolyspora erythraea. Further yield increase is of great importance but requires a better understanding of the underlying physiological processes. Results To reveal the mechanisms related to erythromycin yield increase, we have undertaken an integrated study of the genomic, transcriptomic, and proteomic differences between the wild type strain NRRL2338 (WT) and the industrial high-producing strain ABE1441 (HP) of S. erythraea at multiple time points of a simulated industrial bioprocess. 165 observed mutations lead to differences in gene expression profiles and protein abundance between the two strains, which were most prominent in the initial stages of erythromycin production. Enzymes involved in erythromycin biosynthesis, metabolism of branched chain amino acids and proteolysis were most strongly upregulated in the HP strain. Interestingly, genes related to TCA cycle and DNA-repair were downregulated. Additionally, comprehensive data analysis uncovered significant correlations in expression profiles of the erythromycin-biosynthetic genes, other biosynthetic gene clusters and previously unidentified putative regulatory genes. Based on this information, we demonstrated that overexpression of several genes involved in amino acid metabolism can contribute to increased yield of erythromycin, confirming the validity of our systems biology approach. Conclusions Our comprehensive omics approach, carried out in industrially relevant conditions, enabled the identification of key pathways affecting erythromycin yield and suggests strategies for rapid increase in the production of secondary metabolites in industrial environment.
Ključne besede: aktinomicete, Saccharopolyspora erythraea, sekundarni metaboliti, antibiotiki, eritromicin, biosinteza, metabolno inženirstvo, proteomika
Objavljeno v DiRROS: 25.07.2024; Ogledov: 233; Prenosov: 161
.pdf Celotno besedilo (3,06 MB)
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8.
Moss biomonitoring of the distribution of chemical elements in the air in the Prespa region, North Macedonia
Biljana Dimkova, Robert Šajn, Trajče Stafilov, 2024, izvirni znanstveni članek

Povzetek: A study was conducted to investigate atmospheric deposition and to explore the natural distribution and possible contamination with potentially toxic elements (PTEs) in the Prespa region, North Macedonia, using moss samples as biomonitors for air pollution. The distribution of 19 chemical elements (Ag, Al, Ba, Ca, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Sr, V, and Zn) was detected in 11 moss samples from this area. The moss samples were analysed after microwave digestion using inductively coupled plasma – atomic emission spectrometry (ICP-AES). R-mode factor analysis was used to identify and characterise the elemental associations, and four associations of elements were identified. Four factors were separated from the group of elements: Factor 1 (Fe-Al-Cr-V-Ni), Factor 2 (Sr-Ba-Mg), Factor 3 (K-P-Zn) and Factor 4 (Pb-Cu). All element factors were found to be typical geochemical associations, with the exception of the distribution of K and P in the agricultural areas of the study area where fertilisers are used over a long period of time.
Ključne besede: moss biomonitoring, air pollution, potentially toxic elements, Prespa region, North Macedonia
Objavljeno v DiRROS: 25.07.2024; Ogledov: 187; Prenosov: 154
.pdf Celotno besedilo (1,80 MB)

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High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460
Vera Y. Matrosova, Elena K. Gaidamakova, Kira S. Makarova, Olga Grichenko, Polina Klimenkova, Robert P. Volpe, Rok Tkavc, Gözen Ertem, Isabel H. Conze, Evelyne Brambilla, Nina Gunde-Cimerman, Tine Grebenc, Cene Gostinčar, 2017, izvirni znanstveni članek

Povzetek: The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
Ključne besede: Deinococcus-Thermus, Deinococcaceae, Deinococcus ficus, radiation-resistant, rod-shaped, phenotype characterization, genome analysis, phylogenetic analysis
Objavljeno v DiRROS: 25.07.2024; Ogledov: 227; Prenosov: 160
.pdf Celotno besedilo (1,22 MB)
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