51. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460Vera 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
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53. Stomatal penetration and temporal dynamics of ingress of two fungal isolates associated with leaf spot disease of Jasmine (Jasminum sambac L.)Mark Paul Selda Rivarez, Roy Niño R. Lucila, Pablito M. Magdalita, 2017, izvirni znanstveni članek Povzetek: Jasmine (Jasminum sambac L.) is an ornamental crop grown in South and Southeast Asia for its
flowers for garlands, tea and essential oil production. However, certain fungal foliar and floral diseases
significantly reduce its yield. In this study, Colletotrichum sp.-like (cylindrical conidia) and Fusarium sp.-
like (lunate conidia) isolates causing leaf spot disease were characterized based on the ingression process
and fungal germination in planta. Four-day single-spore cultures in PDA of isolating C1 (Colletotrichum
sp.-like) and F2 (Fusarium sp.-like) were obtained. Suspensions of 108 conidia mL-1 were made and sprayed
onto young leaves of jasmine. Specimen collection was done at 2, 6, 12, 24, 36, 48, 60 and 72 h after
inoculation (hai). Formalin-acetic acid was used to clear the tissues and fungal structures are selectively
stained using lactophenol-acid fuschin. Average ingression sites (IS) were counted for each time point under
50X magnification, then IS per leaf area (cm2) was calculated. Fungal isolates remain at the surface of the
leaf until 36 h. IS of C1 and F2 almost doubled at 48 hai. However, ingression sites declined at 72 hai for
both pathogens, which either imply a progression of sub surface colonization or unsuccessful penetration.
Leaf yellowing and a few spots were observed at 48 hai for F2 and at 60 hai for C1. More severe necrotic
leaf spots with yellow halo (severity rating of 5) were seen in plants inoculated with Fusarium sp.-like
isolated than in those inoculated with Colletotrichum sp.-like isolated. Lastly, at 48 to 60 hai, it was evident
that the pathogen started to seek for stomata, which seemed to be the preferred penetration site for both
fungal pathogens.
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54. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: abiotic factors, abundance, spatial variation, temporal variation
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55. Identification of proteins associated with clinical and pathological features of proliferative diabetic retinopathy in vitreous and fibrovascular membranesIngeborg Klaassen, Ewout W. de Vries, Ilse M.C. Vogels, Antoine H. C. van Kampen, Machteld I. Bosscha, David H. W. Steel, Cornelis J. F. van Noorden, Sarit Y Lesnik-Oberstein, Reinier O. Schlingemann, 2017, izvirni znanstveni članek Povzetek: Purpose
To identify the protein profiles in vitreous associated with retinal fibrosis, angiogenesis, and neurite formation in epiretinal fibrovascular membranes (FVMs) in patients with proliferative diabetic retinopathy (PDR).
Methods
Vitreous samples of 5 non-diabetic control patients with vitreous debris and 7 patients with PDR membranes were screened for 507 preselected proteins using the semi-quantitative RayBio® L-series 507 antibody array. From this array, 60 proteins were selected for a custom quantitative antibody array (Raybiotech, Human Quantibody® array), analyzing 7 control patients, 8 PDR patients with FVMs, and 5 PDR patients without FVMs. Additionally, mRNA levels of proteins of interest were measured in 10 PDR membranes and 11 idiopathic membranes and in retinal tissues and cells to identify possible sources of protein production.
Results
Of the 507 proteins screened, 21 were found to be significantly elevated in PDR patients, including neurogenic and angiogenic factors such as neuregulin 1 (NRG1), nerve growth factor receptor (NGFR), placental growth factor (PlGF) and platelet derived growth factor (PDGF). Angiopoietin-2 (Ang2) concentrations were strongly correlated to the degree of fibrosis and the presence of FVMs in patients with PDR. Protein correlation analysis showed PDGF to be extensively co-regulated with other proteins, including thrombospondin-1 and Ang2. mRNA levels of glial-derived and brain/derived neurotrophic factor (GDNF and BDNF) were elevated in PDR membranes. These results were validated in a second study of 52 vitreous samples of 32 PDR patients and 20 control patients.
Conclusions
This exploratory study reveals protein networks that potentially contribute to neurite outgrowth, angiogenesis and fibrosis in the formation of fibrovascular membranes in PDR. We identified a possible role of Ang2 in fibrosis and the formation of FVMs, and of the neurotrophic factors NRG1, PDGF and GDNF in neurite growth that occurs in all FVMs in PDR.
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56. Cell proliferation on polyethylene terephthalate treated in plasma created in ▫$SO_2/O_2$▫ mixturesNina Recek, Matic Resnik, Rok Zaplotnik, Miran Mozetič, Helena Motaln, Tamara Lah Turnšek, Alenka Vesel, 2017, izvirni znanstveni članek Povzetek: Samples of polymer polyethylene terephthalate were exposed to a weakly ionized gaseous plasma to modify the polymer surface properties for better cell cultivation. The gases used for treatment were sulfur dioxide and oxygen of various partial pressures. Plasma was created by an electrodeless radio frequency discharge at a total pressure of 60 Pa. X-ray photoelectron spectroscopy showed weak functionalization of the samples’ surfaces with the sulfur, with a concentration around 2.5 at %, whereas the oxygen concentration remained at the level of untreated samples, except when the gas mixture with oxygen concentration above 90% was used. Atomic force microscopy revealed highly altered morphology of plasma-treated samples; however, at high oxygen partial pressures this morphology vanished. The samples were then incubated with human umbilical vein endothelial cells. Biological tests to determine endothelialization and possible toxicity of the plasma-treated polyethylene terephthalate samples were performed. Cell metabolic activity (MTT) and in vitro toxic effects of unknown compounds (TOX) were assayed to determine the biocompatibility of the treated substrates. The biocompatibility demonstrated a well-pronounced maximum versus gas composition which correlated well with development of the surface morphology.
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57. A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologiesSébastien Massart, Thierry Candresse, José Gil, Christophe Lacomme, Lukas Predajna, Maja Ravnikar, Jean-Sébastien Reynard, Artemis Rumbou, Pasquale Saldarelli, Dijana Škorić, Eeva J. Vainio, Jari P. T. Valkonen, Hervé Vanderschuren, Christina Varveri, Thierry Wetzel, 2017, izvirni znanstveni članek Povzetek: Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
Ključne besede: NGS, pest risk analysis, virus diseases, biological characterization, plant health, regulatory agencies
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58. Salicylic acid perturbs sRNA-gibberellin regulatory network in immune response of potato to Potato virus Y infectionMaja Križnik, Marko Petek, David Dobnik, Živa Ramšak, Špela Baebler, Stephan Pollmann, Jan F. Kreuze, Jana Žel, Kristina Gruden, 2017, izvirni znanstveni članek Povzetek: Potato virus Y is the most economically important potato viral pathogen. We aimed at unraveling the roles of small RNAs (sRNAs) in the complex immune signaling network controlling the establishment of tolerant response of potato cv. Désirée to the virus. We constructed a sRNA regulatory network connecting sRNAs and their targets to link sRNA level responses to physiological processes. We discovered an interesting novel sRNAs-gibberellin regulatory circuit being activated as early as 3 days post inoculation (dpi) before viral multiplication can be detected. Two endogenous sRNAs, miR167 and phasiRNA931 were predicted to regulate gibberellin biosynthesis genes GA20-oxidase and GA3-oxidase. The increased expression of phasiRNA931 was also reflected in decreased levels of GA3-oxidase transcripts. Moreover, decreased concentration of gibberellin confirmed this regulation. The functional relation between lower activity of gibberellin signaling and reduced disease severity was previously confirmed in Arabidopsis-virus interaction using knockout mutants. We further showed that this regulation is salicylic acid-dependent as the response of sRNA network was attenuated in salicylic acid-depleted transgenic counterpart NahG-Désirée expressing severe disease symptoms. Besides downregulation of gibberellin signaling, regulation of immune receptor transcripts by miR6022 as well as upregulation of miR164, miR167, miR169, miR171, miR319, miR390, and miR393 in tolerant Désirée, revealed striking similarities to responses observed in mutualistic symbiotic interactions. The intertwining of different regulatory networks revealed, shows how developmental signaling, disease symptom development, and stress signaling can be balanced.
Ključne besede: gibberellin, miRNA/siRNA, plant immunity, potato, Potato virus Y, salicylic acid, symbiosis, tolerance
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59. Olfactory signaling of aggressive intent in male-male contests of cave crickets (Troglophilus neglectus; Orthoptera: Rhaphidophoridae)Nataša Stritih Peljhan, Alenka Žunič Kosi, 2017, izvirni znanstveni članek Povzetek: In animal contests, communicating aggressive motivation is most often mediated by visual or acoustic signals, while chemical signals are not expected to serve such a function since they are less able to be modulated by the sender during the changing behavioral context. We describe a rare example of ephemeral olfactory signals in terrestrial animals, signals that are emitted via protrusive scent glands in male cave crickets Troglophilus neglectus (Orthoptera, Rhaphidophoridae) to reflect the state of the signaler’s aggression. We correlate the intensity of behaviorally expressed aggression of the individuals in dyadic contests with the frequency and extent of their gland tissue protrusion, the latter serving as an indication of the amount of released odor. We detected large amounts of odor release during brief gland protrusions, and the absence of its release during gland retraction. Males protruded the glands during and after encountering a rival, with the degree of protrusion increasing with the intensity of the signalers’ aggression. During the encounters, the degree of gland protrusion increased most strongly with the occurrence of the elevated body posture, directly preceding the attack. This degree was significantly higher in encounter winners than in losers displaying such posture, suggesting the highly important role of the released odor for contest resolution. After the encounters, glands were protruded almost exclusively by winners, apparently announcing victory. We tested for the function of the olfactory signals also directly, by preventing gland tissue protrusion in symmetric and asymmetric treatments of the contestants. Treating only the dominant individuals decreased the percentage of encounters they won by over 60%, while treating both contestants elicited a significant increase in the frequency and duration of fights. During contests, the olfactory signals of T. neglectus apparently function as a highly effective threat, which prevents maximal contest escalation and decreases the conflict-related costs.
Ključne besede: animal behaviour, bioacoustics, aggression
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60. ALF : a strategy for identification of unauthorized GMOs in complex mixtures by a GW-NGS method and dedicated bioinformatics analysisAlexandra Bogožalec Košir, Alfred J. Arulandhu, Marleen Voorhuijzen, Hongmei Xiao, Rico Hagelaar, Martijn Staats, Adalberto Costessi, Jana Žel, Esther Kok, Jeroen P. van Dijk, 2017, izvirni znanstveni članek Povzetek: The majority of feed products in industrialised countries contains materials derived from genetically modified organisms (GMOs). In parallel, the number of reports of unauthorised GMOs (UGMOs) is gradually increasing. There is a lack of specific detection methods for UGMOs, due to the absence of detailed sequence information and reference materials. In this research, an adapted genome walking approach was developed, called ALF: Amplification of Linearly-enriched Fragments. Coupling of ALF to NGS aims for simultaneous detection and identification of all GMOs, including UGMOs, in one sample, in a single analysis. The ALF approach was assessed on a mixture made of DNA extracts from four reference materials, in an uneven distribution, mimicking a real life situation. The complete insert and genomic flanking regions were known for three of the included GMO events, while for MON15985 only partial sequence information was available. Combined with a known organisation of elements, this GMO served as a model for a UGMO. We successfully identified sequences matching with this organisation of elements serving as proof of principle for ALF as new UGMO detection strategy. Additionally, this study provides a first outline of an automated, web-based analysis pipeline for identification of UGMOs containing known GM elements.
Ključne besede: biotechnology, molecular biology
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