1. BRCore : an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fittingBolívar Aponte Rolón, Brandon Kristy, Ashley Shade, Nejc Stopnišek, Sarah L. Lebeis, Adina Howe, Niccolo G. M. Benucci, 2026, original scientific article Keywords: microbiome statistics, community ecology, persistent taxa ASV/OTU, ASV/OTU, OTU (Operational Taxonomic Unit), ASV (Amplicon Sequence Variant), abundance-occupancy distributions, Bray-Curtis dissimilarity, Sloan neutral model
Published in DiRROS: 17.06.2026; Views: 221; Downloads: 104
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2. A short-term investigation of diel vertical migrations of the calycophoran Siphonophora in the open south Adriatic Sea (July 2003)Davor Lučić, Adam Benović, Mirna Batistić, Mira Morović, Ivona Onofri, Juan Carlos Molinero, Tjaša Kogovšek, Barbara Gangai, Marijana Miloslavić, 2011, original scientific article Abstract: Morning, midday, evening and night repetitive sampling was used to demonstrate calycophoran diel vertical migration (DVM) at a fixed station in the oligotrophic southern Adriatic Sea at 8 depth intervals. Of 20 calycophoran species collected, most of them inhabited layers of specific temperature and light intensity, and migrated during the night. The deep species Kephyes ovata is primarily non-migratory. Typical nocturnal movements to the surface were recorded for Lensia conoidea and sphaeronectes koellikeri. Lensia subtilis and eudoxoides spiralis migrated toward the surface in the evening but sank deeper at night. Lensia meteori and Lensia fowleri reached upper layers at midday. The DVM of sphaeronectes irregularis was irregular and independent of diel light patterns. Though low in numbers, some calycophorans were found above the thermocline at night. For mesopelagic species, however, higher summer surface temperatures proved an effective barrier to migration above 100 m. Thus, certain species could be represented as key species of planktonic cnidarian assemblages found within a certain depth range. Though not homogenous, and while some undertake nocturnal migrations in both directions, all are interrelated by preferences of bathymetric distribution and specific DVM behavior.
Keywords: sea, medusae, biological research, abundance, bathimetric distribution, siphonophora, calycophoran siphonophores, composition, Adriatic Sea
Published in DiRROS: 26.03.2025; Views: 1034; Downloads: 781
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3. Short-term changes in microbial communities in the water column around the fish farm in the Bay of PiranValentina Turk, Tinkara Tinta, 2021, original scientific article Abstract: A multidisciplinary approach was used to study the impact of fish farming on coastal bacterial communities in the inner part of the Bay of Piran (northern Adriatic). Differences in bacterial abundance, production and the occurrence of selected bacterial groups were studied in the water column around the cage and at different distances from the centre of the fish cage towards the open water, i.e., reference marine station. We also examined the effect of fish feeding on the surrounding system in a short-term in situ experiment based on the simultaneous collection of seawater samples from different locations around the fish cage before and after feeding of fish. Our study suggests that fish feeding has a moderate short-term effect on water column parameters, including bacterial abundance and production, only at a limited distance from the fish cages. The nitrifying, ammonia-oxidizing bacterial groups, as determined by the fluorescent in situ hybridization method, were represented at a higher percentage in the seawater samples in the middle and around the fish cages. β- Proteobacteria, γ-Proteobacteria and the Cytophaga-Flavobacterium group were represented to a higher percentage at sampling sites in the middle of the Bay of Piran and at the reference marine station. The Vibrio group was detected at all sampling sites. The accumulation of organically enriched fish food and waste products released into the seawater during the short-term experiment resulted in a significant increase in particulate matter, orthophosphate and ammonium. In response to the increase in inorganic nutrients, we observed a significant increase in bacterial production, while no significant differences were observed in bacterial abundance in such short time.
Keywords: aquaculture, bacterial abundance, bacterial community composition, bacterial production, fluorescent in situ hybridisation, pollution
Published in DiRROS: 19.03.2025; Views: 952; Downloads: 962
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4. Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis costFilip Buric, Sandra Viknander, Xiaozhi Fu, Oliver Lemke, Oriol Gracia Carmona, Jan Zrimec, Lukasz Szyrwiel, Michael Mülleder, Markus Ralser, Aleksej Zelezniak, 2025, original scientific article Abstract: Understanding what drives protein abundance is essential to biology, medicine, and biotechnology. Driven by evolutionary selection, an amino acid sequence is tailored to meet the required abundance of a proteome, underscoring the intricate relationship between sequence and functional demand. Yet, the specific role of amino acid sequences in determining proteome abundance remains elusive. Here we show that the amino acid sequence alone encodes over half of protein abundance variation across all domains of life, ranging from bacteria to mouse and human. With an attempt to go beyond predictions, we trained a manageable-size Transformer model to interpret latent factors predictive of protein abundances. Intuitively, the model's attention focused on the protein's structural features linked to stability and metabolic costs related to protein synthesis. To probe these relationships, we introduce MGEM (Mutation Guided by an Embedded Manifold), a methodology for guiding protein abundance through sequence modifications. We find that mutations which increase predicted abundance have significantly altered protein polarity and hydrophobicity, underscoring a connection between protein structural features and abundance. Through molecular dynamics simulations we revealed that abundance-enhancing mutations possibly contribute to protein thermostability by increasing rigidity, which occurs at a lower synthesis cost.
Keywords: molecular biology, biotechnology, bioinformatics, deep learning, gene expression, synthetic biology, protein abundance, amino acid sequence, evolutionary selection, transformer model, MGEM (Mutation guided by an embedded manifold)
Published in DiRROS: 17.12.2024; Views: 1628; Downloads: 945
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5. 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: 1567; Downloads: 633
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6. Characterization factors to assess land use impacts on pollinator abundance in life cycle assessmentElizabeth M. Alejandre, Laura Scherer, Jeroen B. Guinée, Marcelo A. Aizen, Matthias Albrecht, Mario V. Balzan, Ignasi Bartomeus, Danilo Bevk, 2023, original scientific article Abstract: While wild pollinators play a key role in global food production, their assessment is currently missing from the most commonly used environmental impact assessment method, Life Cycle Assessment (LCA). This is mainly due to constraints in data availability and compatibility with LCA inventories. To target this gap, relative pollinator abundance estimates were obtained with the use of a Delphi assessment, during which 25 experts, covering 16 nationalities and 45 countries of expertise, provided scores for low, typical, and high expected abundance associated with 24 land use categories. Based on these estimates, this study presents a set of globally generic characterization factors (CFs) that allows translating land use into relative impacts to wild pollinator abundance. The associated uncertainty of the CFs is presented along with an illustrative case to demonstrate the applicability in LCA studies. The CFs based on estimates that reached consensus during the Delphi assessment are recommended as readily applicable and allow key differences among land use types to be distinguished. The resulting CFs are proposed as the first step for incorporating pollinator impacts in LCA studies, exemplifying the use of expert elicitation methods as a useful tool to fill data gaps that constrain the characterization of key environmental impacts.
Keywords: pollinator abundance, ecosystem service, Delphi expert elicitation, agriculture, impact assessment
Published in DiRROS: 12.07.2024; Views: 1475; Downloads: 1022
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