751. SegMine workflows for semantic microarray data analysis in Orange4WSVid Podpečan, Nada Lavrač, Igor Mozetič, Petra Kralj Novak, Igor Trajkovski, Laura Langohr, Kimmo Kulovesi, Hannu Toivonen, Marko Petek, Helena Motaln, Kristina Gruden, 2011, izvirni znanstveni članek Povzetek: Background
In experimental data analysis, bioinformatics researchers increasingly rely on tools that enable the composition and reuse of scientific workflows. The utility of current bioinformatics workflow environments can be significantly increased by offering advanced data mining services as workflow components. Such services can support, for instance, knowledge discovery from diverse distributed data and knowledge sources (such as GO, KEGG, PubMed, and experimental databases). Specifically, cutting-edge data analysis approaches, such as semantic data mining, link discovery, and visualization, have not yet been made available to researchers investigating complex biological datasets.
Results
We present a new methodology, SegMine, for semantic analysis of microarray data by exploiting general biological knowledge, and a new workflow environment, Orange4WS, with integrated support for web services in which the SegMine methodology is implemented. The SegMine methodology consists of two main steps. First, the semantic subgroup discovery algorithm is used to construct elaborate rules that identify enriched gene sets. Then, a link discovery service is used for the creation and visualization of new biological hypotheses. The utility of SegMine, implemented as a set of workflows in Orange4WS, is demonstrated in two microarray data analysis applications. In the analysis of senescence in human stem cells, the use of SegMine resulted in three novel research hypotheses that could improve understanding of the underlying mechanisms of senescence and identification of candidate marker genes.
Conclusions
Compared to the available data analysis systems, SegMine offers improved hypothesis generation and data interpretation for bioinformatics in an easy-to-use integrated workflow environment.
Objavljeno v DiRROS: 05.08.2024; Ogledov: 293; Prenosov: 195
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752. Programmed cell death occurs asymmetrically during abscission in tomatoTal Bar-Dror, Marina Dermastia, Aleš Kladnik, Magda Tušek-Žnidarič, Maruša Pompe Novak, Shimon Meir, Shaul Burd, Sonia Philosoph-Hadas, Naomi Ori, Lilian Sonego, Martin B. Dickman, Amnon Lers, 2011, izvirni znanstveni članek Povzetek: Abscission occurs specifically in the abscission zone (AZ) tissue as a natural stage of plant development. Previously, we observed delay of tomato (Solanum lycopersicum) leaf abscission when the LX ribonuclease (LX) was inhibited. The known association between LX expression and programmed cell death (PCD) suggested involvement of PCD in abscission. In this study, hallmarks of PCD were identified in the tomato leaf and flower AZs during the late stage of abscission. These included loss of cell viability, altered nuclear morphology, DNA fragmentation, elevated levels of reactive oxygen species and enzymatic activities, and expression of PCD-associated genes. Overexpression of antiapoptotic proteins resulted in retarded abscission, indicating PCD requirement. PCD, LX, and nuclease gene expression were visualized primarily in the AZ distal tissue, demonstrating an asymmetry between the two AZ sides. Asymmetric expression was observed for genes associated with cell wall hydrolysis, leading to AZ, or associated with ethylene biosynthesis, which induces abscission. These results suggest that different abscission-related processes occur asymmetrically between the AZ proximal and distal sides. Taken together, our findings identify PCD as a key mechanism that occurs asymmetrically during normal progression of abscission and suggest an important role for LX in this PCD process.
Ključne besede: plant cell, cell death, abscission
Objavljeno v DiRROS: 05.08.2024; Ogledov: 301; Prenosov: 191
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753. Effect of poly-[alpha], [gamma], L-glutamic acid as a capping agent on morphology and oxidative stress-dependent toxicity of silver nanoparticlesMagdalena Stevanović, Branimir Kovačević, Jana Nunić, Metka Filipič, Dragan Uskoković, 2011, izvirni znanstveni članek Povzetek: Highly stable dispersions of nanosized silver particles were synthesized using a straightforward, cost-effective, and ecofriendly method. Nontoxic glucose was utilized as a reducing agent and poly- α, γ, L-glutamic acid (PGA), a naturally occurring anionic polymer, was used as a capping agent to protect the silver nanoparticles from agglomeration and render them biocompatible. Use of ammonia during synthesis was avoided. Our study clearly demonstrates how the concentration of the capping agent plays a major role in determining the dimensions, morphology, and stability, as well as toxicity of a silver colloidal solution. Hence, proper optimization is necessary to develop silver colloids of narrow size distribution. The samples were characterized by Fourier transform infrared spectroscopy, ultraviolet-visible spectroscopy, field-emission scanning electron microscopy, transmission electron microscopy, and zeta potential measurement. MTT assay results indicated good biocompatibility of the PGA-capped silver nanoparticles. Formation of intracellular reactive oxygen species was measured spectrophotometrically using 2,7-dichlorofluorescein diacetate as a fluorescent probe, and it was shown that the PGA-capped silver nanoparticles did not induce intracellular formation of reactive oxygen species.
Ključne besede: green synthesis, morphology, cytotoxicity
Objavljeno v DiRROS: 05.08.2024; Ogledov: 291; Prenosov: 183
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754. Food and feeding habits of the blackspotted smooth-hound, Mustelus punctulatus (Elasmobranchii: carcharhiniformes: Triakidae), from the Northern AdriaticLovrenc Lipej, Borut Mavrič, Snežna Rešek, Mourad Cherif, Christian Capapé, 2011, izvirni znanstveni članek Povzetek: Background. The blackspotted smooth-hound, Mustelus punctulatus Risso, 1826, has been regularly caught in the northern Adriatic Sea, although a decreasing trend in its catches was observed off the coast of Slovenia within the last decade The knowledge of feeding behaviour of elasmobranch fish species, through understanding of the local food web structure, contributes to better and more efficient fish stock assessment and ecosystem modelling. This study is a first step in determining the prey consumption by the blackspotted smooth-hound in the area. Materials and methods. A total of 151 blackspotted smooth-hounds caught by commercial fishermen in the Gulf of Trieste from 4 June 2002 to 4 June 2003 were examined in this study. The stomach contents were removed, sorted and identified to the lowest possible taxon using identification keys. Preys were counted and weighed. Frequency of occurrence (F%), relative abundance (N%), the percentage by weight (W%), the Index of Relative Importance (IRI), and its standardized value (%IRI) were calculated following standard procedures. For comparing the diet between four different size classes we calculate average prey weight, dietary diversity, average meal, and trophic level for each size class. Results. A total 130 fish stomachs contained prey items. Crustaceans were the most important prey items (IRI% = 56.14), whereas cephalopods were the second mostly preyed animals (IRI% = 20.2). Teleost fish and bivalves were also found in the stomachs. The most important prey species was Solecurtus strigillatus. Larger sharks consumed larger preys. Male and female sharks consumed similar food. Juvenile individuals consumed predominantly crustaceans, while cephalopods were more important in the diet of adult individuals. The calculated trophic index (TROPH) of M. punctulatus from northern Adriatic Sea was 3.7, showing that it is a highly carnivorous species. Conclusion. This study is a first step in determining prey consumption by Mustelus punctulatus which is, despite the fact that is still common in the area, a rather poorly known species. For elucidating the role of benthic sharks in the study area the further step would be to study the diet of a closely related common smooth-hound M. mustelus.
Ključne besede: fishes, ichthyology, Adriatic sea, Triakidae, Mustelus punctulatus, trophic level, northern Adriatic, elasmobranchii, diversity, Mustelus, Mediterranean, feeding, Adriatic Sea
Objavljeno v DiRROS: 05.08.2024; Ogledov: 312; Prenosov: 212
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755. cis-vaccenyl acetate, a female-produced sex pheromone component of Ortholeptura valida, a longhorned beetle in the subfamily LepturinaeAnn M. Ray, Alenka Žunič Kosi, Ronald L. Alten, J. Steven McElfresh, Lawrence M. Hanks, Jocelyn G. Millar, 2011, izvirni znanstveni članek Povzetek: We report the identification, synthesis, and field bioassays of a female-produced sex attractant pheromone component of the cerambycid beetle Ortholeptura valida (LeConte). Headspace volatiles from females contained a female-specific compound, (Z)-11-octadecen-1-yl acetate, which elicited a strong response from antennae of adult males in coupled gas chromatography-electroantennogram analyses. In field bioassays, significant numbers of males were collected by traps baited with this compound. The pheromone represents a new structural class of cerambycid pheromones, and is the first pheromone identified for a cerambycid species in the subfamily Lepturinae.
Ključne besede: sex pheromone, (Z)-11-octadecen-1-yl ac, cis-vaccenyl acetate, woodborer
Objavljeno v DiRROS: 05.08.2024; Ogledov: 288; Prenosov: 155
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756. Potential solutions for ▫$CO_2▫$-capturing technologies in the slovenian contextJanvit Golob, Dušan Klinar, Mihael Bricelj, 2012, izvirni znanstveni članek Povzetek: Human activities have caused an enormous rise of the CO2 concentration in the Earth’s atmosphere over the past 200 years. In order to alleviate this problem, the threats to and the concerns of the international community need to be converted into economic opportunities for national economies, which shall develop and utilize technological opportunities rather than simply accepting international obligations to reduce CO2 emissions. In the article we analyze technological possibilities in the Slovenian context as possible opportunities for promoting sustainable development based on regional, renewable resources. Beginning with an analysis of the amine process for CO2 concentration and its possibilities, we continue with CO2 chemistry examples, like the precipitation of calcium carbonate from Ca++ sources like lime or fly ash. Through the concept of product engineering we emphasize the need for a stepwise realization from the laboratory to a pilot plant and then to the industrial scale. The growth of biomass through forestry or algae production can provide an additional CO2 sink. However, for an efficient technical solution and implementation a close working relationship between biologists and engineers is required.
Ključne besede: CO2 minimization, technological opportunities, amine concentration, CO2 chemistry, forestry, algae production, fly ash CO2 absorption
Objavljeno v DiRROS: 05.08.2024; Ogledov: 274; Prenosov: 199
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757. The Ural Owl, Strix uralensis macroura, in Slovenia : an overview of current knowledge on species ecologyAl Vrezec, Tomaž Mihelič, 2012, izvirni znanstveni članek Povzetek: In Slovenia the Ural Owl, Strix uralensis macroura, is on the north-western limit of its distribution with an estimated population size of 400-700 breeding pairs. The densities of territories range between 0.9 to 13.4 territories per 10 km2, and the highest densities are reached in montane forests of the southern Dinaric region. In the forests with dominant deciduous trees, e.g. Fagus sylvatica and Quercus robur, the breeding densities are significantly higher than in the forests with a higher proportion of coniferous trees, e.g. Picea abies. The species does not select specific altitude and throughout Slovenia it occurs between 150 and 1600 m a.s.l. Most natural nests were found in tree holes or semi-holes (56%) and on the tree stumps (20%). Breeding begins between 15 March to 21 June with median clutch sizes of 3.0 eggs per nest. In the brood there are 2 young and 1.5 young are fledged in median. At present 75% of nests produce at least one young. Voles and Mice are the most frequent prey in the diet, but the Fat Dormouse, Glis glis, seems to have very important role in the post-breeding period. As a top predator, the Ural Owl influences also the distribution of other owl species in the guild through direct predation or competitive exclusion. However, it could have also a positive indirect effect on smaller species, e.g. Tengmalm’s Owl, Aegolius funereus, which are tolerated within Ural Owl territories, and are able to extend their distribution due to exclusion from certain areas of the Tawny Owl, Strix aluco, by the Ural Owl.
Ključne besede: distribution, breeding density, habitat, breeding biology, interactions, Slovenia
Objavljeno v DiRROS: 05.08.2024; Ogledov: 274; Prenosov: 192
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759. Interannual size changes of adult Aurelia sp.5 medusae stage in the Marine protected Area of Mljet Island South AdriaticTjaša Kogovšek, Juan Carlos Molinero, Davor Lučić, Ivona Onofri, Barbara Gangai, Marijana Miloslavić, Delphine Bonnet, Alenka Malej, 2012, izvirni znanstveni članek Povzetek: Aurelia aurita s.l. is the most widespread scyphozoan jellyfish that recurrently appear “en mass” and forms large aggregations mainly in coastal waters, embayments and estuaries. Beside anthropogenic factors controlling jellyfish populations climate change may play an important role. The aim of this study was to assess whether climate-related factors in absence of other anthropogenically induced stressor influence medusae size. We investigated seasonal and interannual changes in the size of Aurelia in a “jelly lake” in the National Park of Mljet Island (Croatia) where minimal human impact on the environment makes the Veliko Jezero a natural mesocosm for understanding the impact of climate change on the Aurelia population. The observed changes suggest Aurelia medusa population response to changing environment, in particular to enhanced temperature, by reduced body sizes. Comparison of Aurelia population dynamics from different regions in the Mediterranean Sea revealed the unique feature of the Veliko Jezero population. Despite the similarity of the environmental windows of medusae occurrences in the Veliko Jezero and regions in the Mediterranean Sea, medusae in the Veliko Jezero are present all year round. It seems that the lake bathymetry enables medusae to vertically migrate to deeper and cooler water layer, avoiding the limiting temperatures developed in the upper layer during the summer. These conditions may prolong the Aurelia medusae life span and together with continuous strobilation support the stability of the Aurelia medusae population all year round.
Ključne besede: Mediterraneum, moon jellyfish, Adriatic Sea, South Adriatic Sea, marine lakes, Aurelia spp, climate-related factor, Mediterranean Sea, marine research, population dynamics
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760. The epiplankton community in the southern Adriatic: multiple trophic levels along the south - north and inshore-offshore gradientsValentina Turk, Davor Lučić, Jakica Njire, Senka Terzić, Tinkara Tinta, Adam Benović, Alenka Malej, 2012, izvirni znanstveni članek Povzetek: The epiplankton community was investigated during Meduza cruises along south - north and offshore – inshore transects in the middle and southern Adriatic in spring 2002. The diel and vertical distribution of heterotrophic bacteria, phytoplankton pigment composition, micro- and mesozooplankton were assessed. At most stations we observed a thermocline at approximately 20 m and a prominent chlorophyll a peak at about 70 m depth. The integrated phytoplankton and bacterial biomass were lower at the station in the central part of the southern Adriatic, and increased gradually towards middle Adriatic and towards coastal stations. Vertical profiles of both bacterial abundance and production showed a distinct peak in the surface layer. Bacterial abundance was high also in the layer of the deep chlorophyll a maximum. Higher bacterial production was associated with elevated abundance of pico- and nanoplankton feeding zooplankton indicating that bacterial populations were generally controlled by predation.
Ključne besede: Meduza project, heterotrophic bacteria, Adriatic Sea, South Adriatic Sea, phytoplankton pigments, open sea, microzooplankton, mesozooplankton, research cruises
Objavljeno v DiRROS: 05.08.2024; Ogledov: 305; Prenosov: 158
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