1. Exceptional dense water formation on the Adriatic shelf in the winter of 2012Hrvoje Mihanović, Ivica Vilibić, S. Carniel, M. Tudor, A. Russo, A. Bergamasco, N. Bubić, Z. Ljubešić, Damir Viličić, A. Boldrin, Vlado Malačič, Massimo Celio, Cinzia Comici, F. Raicich, 2013, izvirni znanstveni članek Povzetek: In this paper we document dense water formation throughout the Adriatic shelf and coastal area in January/February 2012, resulting in record-breaking densities observed during and after the event. The unprecedented dense water generation was preconditioned by a dry and warm year which resulted in a significant reduction of coastal freshwaters, superimposed on a long-term basin-wide salinity increase. The final event that triggered the dense water formation was an extended period of cold weather with strong and severe winds. Record-breaking potential density anomalies (above 30 kg m−3) were measured at several formation sites. Accumulated surface net heat and water losses in some coastal regions exceeded 1.5 GJ m−2 and 250 kg m−2 over 21 days, respectively. Excessiveness, importance of shelf-type dense water formation and effects on the thermohaline circulation and deep aquatic systems are discussed.
Ključne besede: sea, marine water, density, physical oceanography, dense water, water density, Adriatic sea, Mediterranean sea, Adriatic shelf
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2. Structural and functional responses of harpacticoid copepods to anoxia in the Northern Adriatic: an experimental approachMarleen Roelofs, Marleen De Troch, Bettina Riedel, Mateja Grego, 2013, izvirni znanstveni članek Povzetek: Combined in situ and laboratory studies were conducted to document the effects of anoxia on the structure and functioning of meiobenthic communities, with special focus on harpacticoid copepods. In a first step, anoxia was created artificially by means of an underwater chamber at 24 m depth in the Northern Adriatic, Gulf of Trieste (Mediterranean). Nematodes were found as the most abundant taxon, followed by harpacticoid copepods. While nematode densities were not affected by treatment (anoxia/normoxia) or sediment depth, these factors had a significant impact on copepod abundances. Harpacticoid copepod family diversity, in contrast, was not affected by anoxic conditions, only by depth. Ectinosomatidae and Cletodidae were most abundant in both normoxic and anoxic samples.
The functional response of harpacticoid copepods to anoxia was studied in a laboratory tracer experiment by adding 13C pre-labelled diatoms to sediment cores in order to test (1) if there is a difference in food uptake by copepods under normoxic and anoxic conditions and (2) whether initial (normoxia) feeding of harpacticoid copepods on diatoms results in a better survival of copepods in subsequent anoxic conditions. Independent of the addition of diatoms, there was a higher survival rate in normoxia than anoxia. The supply of additional food did not result in a higher survival rate of copepods in anoxia, which might be explained by the presence of a nutritionally better food source and/or a lack of starvation before adding the diatoms. However, there was a reduced grazing pressure by copepods on diatoms in anoxic conditions. This resulted in a modified fatty acid composition of the sediment. We concluded that anoxia not only impacts the survival of consumers (direct effect) but also of primary producers (indirect effect), with important implications for the recovery phase.
Ključne besede: morje, plankton, kopepodi, živalski plankton, trofični status, morski plankton, harpaktikoidi, anoksije
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3. CellTracker Green labelling vs. Rose Bengal staining: CTG wins by points in distinguishing living from dead anoxia-impacted copepods and nematodsMateja Grego, Michael Stachowitsch, Marleen De Troch, Bettina Riedel, 2013, izvirni znanstveni članek Povzetek: Hypoxia and anoxia have become a key threat to shallow coastal seas. Much is known about their impact on macrofauna, less on meiofauna. In an attempt to shed more light on the latter group, in particular from a process-oriented view, we experimentally induced short-term anoxia (1 week) in the northern Adriatic Sea (Mediterranean) and examined the two most abundant meiofauna taxa – harpacticoid copepods and nematodes. Both taxa also represent different ends of the tolerance spectrum, with copepods being the most sensitive and nematodes among the most tolerant. We compared two methods: CellTracker Green (CTG) – new labelling approach for meiofauna – with the traditional rose bengal (RB) staining method. CTG binds to active enzymes and therefore colours live organisms only. The two methods show considerable differences in the number of living and dead individuals of both meiofauna taxa. Generally, RB will stain dead but not yet decomposed copepods and nematodes equally as it does live ones. Specifically, RB significantly overestimated the number of living copepods in all sediment layers in anoxic samples, but not in any normoxic samples. In contrast, for nematodes, the methods did not show such a clear difference between anoxia and normoxia. RB overestimated the number of living nematodes in the top sediment layer of normoxic samples, which implies an overestimation of the overall live nematofauna. For monitoring and biodiversity studies, the RB method might be sufficient, but for more precise quantification of community degradation, especially after an oxygen depletion event, CTG labelling is a better tool. Moreover, it clearly highlights the surviving species within the copepod or nematode community. As already accepted for foraminiferal research, we demonstrate that the CTG labelling is also valid for other meiofauna groups.
Ključne besede: morje, plankton, kopepodi, živalski plankton, trofični status, morski plankton, CTG, CellTracker Green
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4. Vloga matičnih celic pri napredovanju in zdravljenju gliomaUrška Verbovšek, Tamara Lah Turnšek, Helena Motaln, Mateja Robič, 2013, izvirni znanstveni članek Povzetek: Izvor tumorjev in stohastično naravo procesa karcinogeneze najbolje opisuje hierarhični model, ki predvideva obstoj tumorskih matičnih celic (TMC). Slednje predstavljajo populacijo celic z neomejenim samoobnovitvenim potencialom, ki so se sposobne diferencirati v vrste celic vseh treh zarodnih linij in so manj občutljive na večino protirakavih učinkovin. Zato predstavljajo glavni vir za razvoj in rast tumorja, zaradi svoje odpornosti na kemoterapijo pa so vzrok za ponovitev bolezni. Za uspešno zdravljenje možganskega tumorja glioma in njegove najbolj maligne oblike, glioblastoma multiformae (GBM), bi zato bilo potrebno odstraniti prav vse TMC. Žal slednjega zaradi prehitre infiltrativne vrasti subpopulacije GBM celic z visoko izraženimi geni za gibljivost (migratom) v okolno zdravo možgansko tkivo, ni možno doseči s trenutno uporabljanimi načini zdravljenja (npr. kirurškim izrezom)
Poleg TMC, ki so ključne za razvoj in razrast tumorja, tkivo tumorja vsebuje še hematopoetske matične celice, endotelne predniške celice in mezenhimske matične celice (MMC). Delovanje teh drugih vrst matičnih celic, kjer je bila celicam MMC že dokazana protitumorska aktivnost v GBM, pa je odvisno od tumorskega mikrookolja. Žal mehanizmi in delovanje MMC med modulacijo rasti tumorja preko parakrinih in neposrednih interakcij z GBM (matičnimi) celicami še niso znani. Kljub temu pa matične celice, s poudarkom na MMC, predstavljajo nove nosilce npr. za ciljni vnos terapevtske učinkovine v tumor, ki bi lahko izboljšali učinkovitost trenutnih protitumorskih terapij. Razvoj celičnih zdravil veliko obeta, saj so MMC, poleg svojih imunomodulacijskih lastnosti, sposobne tudi usmerjenega gibanja v GBM in tam učinkovati, o čemer razpravlja ta prispevek.
Ključne besede: tumorske matične celice, mezenhimske matične celice, mikrookolje tumorja, celična terapija
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5. Identification of plasma biomarker candidates in glioblastoma using an antibody-array-based proteomic approachKlemen Zupančič, Marjan Koršič, Urška Verbovšek, Primož Rožman, Tamara Lah Turnšek, Andrej Blejec, Kristina Gruden, Helena Motaln, Miomir Knežević, Matija Veber, Ana Herman, 2014, izvirni znanstveni članek Povzetek: Background. Glioblastoma multiforme (GBM) is a brain tumour with a very high patient mortality rate, with a median survival of 47 weeks. This might be improved by the identification of novel diagnostic, prognostic and predictive
therapy-response biomarkers, preferentially through the monitoring of the patient blood. The aim of this study was to define the impact of GBM in terms of alterations of the plasma protein levels in these patients.
Materials and methods. We used a commercially available antibody array that includes 656 antibodies to analyse
blood plasma samples from 17 healthy volunteers in comparison with 17 blood plasma samples from patients with
GBM.
Results. We identified 11 plasma proteins that are statistically most strongly associated with the presence of GBM.
These proteins belong to three functional signalling pathways: T-cell signalling and immune responses; cell adhesion and migration; and cell-cycle control and apoptosis. Thus, we can consider this identified set of proteins as potential diagnostic biomarker candidates for GBM. In addition, a set of 16 plasma proteins were significantly associated with the overall survival of these patients with GBM. Guanine nucleotide binding protein alpha (GNAO1) was associated with both GBM presence and survival of patients with GBM.
Conclusions. Antibody array analysis represents a useful tool for the screening of plasma samples for potential cancer biomarker candidates in small-scale exploratory experiments; however, clinical validation of these candidates requires their further evaluation in a larger study on an independent cohort of patients.
Ključne besede: glioblastoma, proteomics, biomarker
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6. New records of opistobranch gastropods in the waters off Slovenia (Gulf of Trieste, Northern Adriatic Sea)Lovrenc Lipej, Borut Mavrič, Jan Simič, Domen Trkov, 2014, izvirni znanstveni članek Povzetek: The paper deals with four opisthobranch molluscs, which were found in the Slovenian marine waters as new records. The pleurobranchomorph Pleurobranchea meckeli was found on two occasions on muddy detritic bottom in the Gulf of Piran in June of 2013 and 2014. The nudibranch Favorinus branchialis was found in May and June 2014 on turf vegetation in a very shallow area off the pier in Koper harbour. Its spawn with white eggs was also found nearby. The second nudibranch Facelina rubrovittata was found in March 2010 crawling in the intertidal zone of the Nature reserve Strunjan. The third nudibranch Dondice banyulensis was found in waters of the Nature Monument Debeli rtic on sedimentary bottom. With the fi nding of these four species, the total number of opisthobranchs recorded to date in the Slovenian part of the Adriatic Sea increased to 75 species.
Ključne besede: opistobranch fauna, sea, Slovenia, Mediterranean Sea, Gulf of Trieste
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7. The lesser-known medusa Drymonema dalmatinum Haeckel 1880 (Scyphozoa, Discomedusae) in the Adriatic SeaAlenka Malej, Martin Vodopivec, Davor Lučić, Ivona Onofri, Branka Pestorić, 2014, izvirni znanstveni članek Povzetek: Authors report historical and recent records of the little-known medusa Drymonema dalmatinum in the Adriatic
Sea. This large scyphomedusa, which may develop a bell diameter of more than 1 m, was fi rst described in 1880 by
Haeckel based on four specimens collected near the Dalmatian island Hvar. The paucity of this species records since
its description confi rms its rarity, however, in the last 15 years sightings of D. dalmatinum have been more frequent.
Ključne besede: scyphomedusae, historical occurrence, recent observations, Adriatic Sea
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8. Recurrence of Sargassum vulgare C. Agardh in Slovenian coastal waters (Adriatic Sea)Martina Orlando-Bonaca, Borut Mavrič, 2014, izvirni znanstveni članek Povzetek: Perennial species from the genus Sargassum are considered to be indicators of high environmental quality and are therefore used in the assessment of the Ecological Status of Mediterranean coastal waters according to the European Water Framework Directive (WFD, 2000/60/EC). Over the past three decades a signifi cant decline in Sargassum populations has been reported in the Gulf of Trieste, as well as in other Adriatic and Mediterranean areas. In Slovenian coastal waters the presence of Sargassum spp. had not been confi rmed since 1980, after a severe decline due to overgrazing by the sea urchin Paracentrotus lividus. Recently, however, some thalli of S. vulgare were found in Piran Bay. The recurrence of this species is discussed in the paper, as well as the possible causes that led to the non-recovery in its populations in last decades in Slovenian coastal waters.
Ključne besede: macroalgae, Gulf of Trieste, Sargassum, Mediterranean Sea, non-recovery of populations
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9. Reverse transcriptase droplet digital PCR shows high resilience to PCR inhibitors from plant, soil and water samplesNejc Rački, Tanja Dreo, Ion Gutiérrez-Aguirre, Andrej Blejec, Maja Ravnikar, 2014, izvirni znanstveni članek Povzetek: Background
Detection and quantification of plant pathogens in the presence of inhibitory substances can be a challenge especially with plant and environmental samples. Real-time quantitative PCR has enabled high-throughput detection and quantification of pathogens; however, its quantitative use is linked to standardized reference materials, and its sensitivity to inhibitors can lead to lower quantification accuracy. Droplet digital PCR has been proposed as a method to overcome these drawbacks. Its absolute quantification does not rely on standards and its tolerance to inhibitors has been demonstrated mostly in clinical samples. Such features would be of great use in agricultural and environmental fields, therefore our study compared the performance of droplet digital PCR method when challenged with inhibitors common to plant and environmental samples and compared it with quantitative PCR.
Results
Transfer of an existing Pepper mild mottle virus assay from reverse transcription real-time quantitative PCR to reverse transcription droplet digital PCR was straight forward. When challenged with complex matrices (seeds, plants, soil, wastewater) and selected purified inhibitors droplet digital PCR showed higher resilience to inhibition for the quantification of an RNA virus (Pepper mild mottle virus), compared to reverse transcription real-time quantitative PCR.
Conclusions
This study confirms the improved detection and quantification of the PMMoV RT-ddPCR in the presence of inhibitors that are commonly found in samples of seeds, plant material, soil, and wastewater. Together with absolute quantification, independent of standard reference materials, this makes droplet digital PCR a valuable tool for detection and quantification of pathogens in inhibition prone samples.
Ključne besede: PCR amplification, inhibition, qPCR, droplet digital PCR, environmental samples
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10. TRIM28 and [beta]-actin identified via nanobody-based reverse proteomics approach as possible human glioblastoma biomarkersIvana Jovchevska, Neja Šamec, Nina Kočevar Britovšek, Daniela Cesselli, Neža Podergajs, Clara Limbaeck Stanic, Michael P. Myers, Serge Muyldermans, Gholamreza Hassanzadeh Ghassabeh, Helena Motaln, Maria Elisabetta Ruaro, Evgenia Bourkoula, Tamara Lah Turnšek, Radovan Komel, 2014, izvirni znanstveni članek Povzetek: Malignant gliomas are among the rarest brain tumours, and they have the worst prognosis. Grade IV astrocytoma, known as glioblastoma multiforme (GBM), is a highly lethal disease where the standard therapies of surgery, followed by radiation and chemotherapy, cannot significantly prolong the life expectancy of the patients. Tumour recurrence shows more aggressive form compared to the primary tumour, and results in patient survival from 12 to 15 months only. Although still controversial, the cancer stem cell hypothesis postulates that cancer stem cells are responsible for early relapse of the disease after surgical intervention due to their high resistance to therapy. Alternative strategies for GBM therapy are thus urgently needed. Nanobodies are single-domain antigen-binding fragments of heavy-chain antibodies, and together with classical antibodies, they are part of the camelid immune system. Nanobodies are small and stable, and they share a high degree of sequence identity to the human heavy chain variable domain, and these characteristics offer them advantages over classical antibodies or antibody fragments. We first immunised an alpaca with a human GBM stem-like cell line prepared from primary GBM cultures. Next, a nanobody library was constructed in a phage-display vector. Using nanobody phage-display technology, we selected specific GBM stem-like cell binders through a number of affinity selections, using whole cell protein extracts and membrane protein-enriched extracts from eight different GBM patients, and membrane protein-enriched extracts from two established GBM stem-like cell lines (NCH644 and NCH421K cells). After the enrichment, periplasmic extract ELISA was used to screen for specific clones. These nanobody clones were recloned into the pHEN6 vector, expressed in Escherichia coli WK6, and purified using immobilised metal affinity chromatography and size-exclusion chromatography. Specific nanobody:antigen pairs were obtained and mass spectrometry analysis revealed two proteins, TRIM28 and β-actin, that were up-regulated in the GBM stem-like cells compared to the controls.
Ključne besede: malignant gliomas, cancer stem cells, nanobodies
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