641. Ecological patterns of polychaete assemblages associated with the Mediterranean stony coral Cladocora caespitosa (Linnaeus, 1767) : a comparison of sites in two biogeographic zones (Adriatic and Aegean Sea)Valentina Pitacco, Giorgos Chatzigeorgiou, Barbara Mikac, Lovrenc Lipej, 2021, original scientific article Abstract: The Mediterranean stony coral Cladocora caespitosa (Linnaeus, 1767) is a well-known habitat builder, and as such hosts a diversified faunal assemblage. Although polychaetes are one of the most abundant and diverse macrobenthic groups associated with C. caespitosa colonies, our knowledge of their ecological features in this association is still limited. The aim of this paper was to gather and compare the most comprehensive data available on polychaetes associated with C. caespitosa in the Adriatic and the Aegean Seas, and to test for differences between these geographic areas. To this end, differences were tested in terms of: (i) richness and structure of polychaete assemblages; (ii) feeding and functional traits of assemblages; (iii) the main factors influencing those aspects, (iv) the relationship between polychaete assemblages richness and Cladocora colony size, and estimate richness. Differences were observed between the Adriatic and the Aegean Seas, in terms of richness, species composition and relative proportion of the dominant feeding guild (filter feeders most abundant in the Aegean and carnivores in the Adriatic) and motility mode (sessile most abundant in the Aegean and motile in the Adriatic). Conversely, cosmopolitan and Atlanto-Mediterranean species dominated the assemblages in both geographic areas, and the same Species-Area Relation model proved to be effective for richness estimation in both geographic areas. Keywords: benthic ecology, habitat builder species, polychaeta, Mediterranean Sea Published in DiRROS: 19.07.2024; Views: 120; Downloads: 49
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642. Stratification strength and light climate explain variation in chlorophyll a at the continental scale in a European multilake survey in a heatwave summerDaphne Donis, Evanthia Mantzouki, Daniel F. McGinnis, Dominic Vachon, Irene Gallego, Hans-Peter Grossart, Lisette N. de Senerpont Domis, Sven Teurlincx, Laura Seelen, Miquel Lürling, Špela Remec-Rekar, Tina Eleršek, 2021, original scientific article Abstract: To determine the drivers of phytoplankton biomass, we collected standardized morphometric, physical, and biological data in 230 lakes across the Mediterranean, Continental, and Boreal climatic zones of the European continent. Multilinear regression models tested on this snapshot of mostly eutrophic lakes (median total phos-phorus [TP]=0.06 and total nitrogen [TN]=0.7 mg L1), and its subsets (2 depth types and 3 climatic zones), show that light climate and stratification strength were the most significant explanatory variables for chloro-phylla(Chla) variance. TN was a significant predictor for phytoplankton biomass for shallow and continental lakes, while TP never appeared as an explanatory variable, suggesting that under high TP, light, which partially controls stratification strength, becomes limiting for phytoplankton development. Mediterranean lakes were the warmest yet most weakly stratified and had significantly less Chlathan Boreal lakes, where the temperature anomaly from the long-term average, during a summer heatwave was the highest (+4C) and showed a signifi-cant, exponential relationship with stratification strength. This European survey represents a summer snapshotof phytoplankton biomass and its drivers, and lends support that light and stratification metrics, which are bothaffected by climate change, are better predictors for phytoplankton biomass in nutrient-rich lakes than nutrient concentrations and surface temperature. Published in DiRROS: 19.07.2024; Views: 116; Downloads: 115
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643. A phase Ib clinical trial of metformin and chloroquine in patients with IDH1-mutated solid tumorsMohammed Khurshed, Remco J. Molenaar, Myra E van Linde, Ron A Mathôt, Eduard A. Struys, Tom van Wezel, Cornelis J. F. van Noorden, Heinz-Josef Klümpen, Judith V. M. G. Bovée, Johanna W Wilmink, 2021, original scientific article Abstract: Background: Mutations in isocitrate dehydrogenase 1 (IDH1) occur in 60% of chondrosarcoma, 80% of WHO grade II-IV glioma and 20% of intrahepatic cholangiocarcinoma. These solid IDH1-mutated tumors produce the oncometabolite D-2-hydroxyglutarate (D-2HG) and are more vulnerable to disruption of their metabolism. Methods: Patients with IDH1-mutated chondrosarcoma, glioma and intrahepatic cholangiocarcinoma received oral combinational treatment with the antidiabetic drug metformin and the antimalarial drug chloroquine. The primary objective was to determine the occurrence of dose-limiting toxicities (DLTs) and the maximum tolerated dose (MTD). Radiological and biochemical tumor responses to metformin and chloroquine were investigated using CT/MRI scans and magnetic resonance spectroscopy (MRS) measurements of D-2HG levels in serum. Results: Seventeen patients received study treatment for a median duration of 43 days (range: 7–74 days). Of twelve evaluable patients, 10 patients discontinued study medication because of progressive disease and two patients due to toxicity. None of the patients experienced a DLT. The MTD was determined to be 1500 mg of metformin two times a day and 200 mg of chloroquine once a day. A serum D/L-2HG ratio of ≥4.5 predicted the presence of an IDH1 mutation with a sensitivity of 90% and a specificity of 100%. By utilization of digital droplet PCR on plasma samples, we were able to detect tumor-specific IDH1 hotspot mutations in circulating tumor DNA (ctDNA) in investigated patients. Conclusion: Treatment of advanced IDH1-mutated solid tumors with metformin and chloroquine was well tolerated but did not induce a clinical response in this phase Ib clinical trial. Keywords: metformin, chloroquine, cancer, isocitrate dehydrogenase, pharmacokinetics, glioblastoma, intrahepatic cholangiocarcinoma, chondrosarcoma Published in DiRROS: 19.07.2024; Views: 112; Downloads: 112
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644. Plastic-degrading potential across the global microbiome correlates with recent pollution trendsJan Zrimec, Mariia Kokina, Sara Jonasson, Aleksej Zelezniak, Francisco Zorrilla, 2021, original scientific article Abstract: Biodegradation is a plausible route toward sustainable management of the millions of tons of plastic waste that have accumulated in terrestrial and marine environments. However, the global diversity of plastic-degrading enzymes remains poorly understood. Taking advantage of global environmental DNA sampling projects, here we constructed hidden Markov models from experimentally verified enzymes and mined ocean and soil metagenomes to assess the global potential of microorganisms to degrade plastics. By controlling for false positives using gut microbiome data, we compiled a catalogue of over 30,000 nonredundant enzyme homologues with the potential to degrade 10 different plastic types. While differences between the ocean and soil microbiomes likely reflect the base compositions of these environments, we find that ocean enzyme abundance increases with depth as a response to plastic pollution and not merely taxonomic composition. By obtaining further pollution measurements, we observed that the abundance of the uncovered enzymes in both ocean and soil habitats significantly correlates with marine and country-specific plastic pollution trends. Our study thus uncovers the earth microbiome's potential to degrade plastics, providing evidence of a measurable effect of plastic pollution on the global microbial ecology as well as a useful resource for further applied research. Published in DiRROS: 19.07.2024; Views: 121; Downloads: 101
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645. On-farm experiences shape farmer knowledge, perceptions of pollinators, and management practicesJulia Osterman, Patricia Landaverde-González, Michael P. D. Garratt, Megan Gee, Yael Mandelik, Aleksandra Langowska, Marcos Miñarro, Lorna J. Cole, Maxime Eeraerts, Danilo Bevk, 2021, original scientific article Abstract: Mitigating pollinator declines in agriculturally dominated landscapes to safeguard pollination services requires the involvement of farmers and their willingness to adopt pollinator-friendly management. However, farmer knowledge, perceptions, and actions to support on-farm pollinators and their alignment with science-based knowledge and recommendations are rarely evaluated. To close this knowledge gap, we interviewed 560 farmers from 11 countries around the world, cultivating at least one of four widely grown pollinator-dependent crops (apple, avocado, kiwifruit, oilseed rape). We particularly focused on non-bee crop pollinators which, despite being important pollinators of many crops, received less research attention than bees. We found that farmers perceived bees to be more important pollinators than other flower-visiting insects. However, around 75% of the farmers acknowledged that non-bees contributed to the pollination of their crops, seeing them as additional pollinators rather than substitutes for bees. Despite farmers rating their own observations as being most important in how they perceived the contribution of different crop pollinator taxa, their perception aligned closely with results from available scientific studies across crops and countries. Farmer perceptions were also linked with their pollinator management practices, e.g. farmers who used managed bees for crop pollination services (more than half the farmers) rated these managed bees as particularly important. Interestingly, their willingness to establish wildflower strips or manage hedgerows to enhance pollinator visitation was linked to their ecological knowledge of non-bees or to government subsidies. Farmers adapted practices to enhance pollination services depending on the crop, which indicates an understanding of differences in the pollination ecology of crops. Almost half of the farmers had changed on-farm pollination management in the past 10 years and farm practices differed greatly between countries. This suggests integrated crop pollination measures are being adapted by farmers to reach best pollinator management practices. Our findings highlight the importance of studying local knowledge as a key to co-design locally-adapted measures to facilitate pollinator-integrated food production as ecological intensification tools. Keywords: conservation, crop pollination, ecological intensification, farmer knowledge, local knowledge, survey Published in DiRROS: 19.07.2024; Views: 136; Downloads: 119
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646. Biogeography of Long-Jawed Spiders Reveals Multiple Colonization of the CaribbeanKlemen Čandek, Ingi Agnarsson, Greta Binford, Matjaž Kuntner, 2021, original scientific article Abstract: Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested this prediction on long-jawed spiders (Tetragnatha) of the Caribbean archipelago using phylogenies from a total of 318 individuals delineated into 54 putative species. Our results support a Tetragnatha monophyly (within our sampling) but reject the monophyly of the Caribbean lineages, where we found low endemism yet high diversity. The reconstructed biogeographic history detects a potential early overwater colonization of the Caribbean, refuting an ancient vicariant origin of the Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, the results imply multiple colonization events to and from the Caribbean from the mid-Eocene to late-Miocene. Among arachnids, Tetragnatha uniquely comprises both excellently and poorly dispersing species. A direct test of the IDM would require consideration of three categories of dispersers; however, long-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes. A taxon such as Tetragnatha, one that readily undergoes evolutionary changes in dispersal propensity, can be referred to as a ‘dynamic disperser’. Keywords: Tetragnatha, dynamic disperser, intermediate dispersal model of biogeography, GAARlandia Published in DiRROS: 19.07.2024; Views: 110; Downloads: 27
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647. Hay meadow vibroscape and interactions within insect vibrational communityRok Šturm, Behare Rexhepi, Juan José López Díez, Andrej Blejec, Jernej Polajnar, Jérôme Sueur, Meta Virant-Doberlet, 2021, original scientific article Abstract: Our experiences shape our knowledge and understanding of the world around us. The natural vibrational environment (vibroscape) is hidden to human senses but is nevertheless perceived and exploited by the majority of animals. Here, we show that the vibroscape recorded on plants in a temperate hay meadow is a dynamic low-frequency world, rich in species-specific vibrational signals. The overall vibroscape composition changed throughout the season and also depended on the plant species, as well as on the spatial position of individual plants within the meadow. Within the studied community, vibrationally signaling species sharing this communication channel avoided interference primarily by partitioning vibrational space on a fine temporal scale. The vibroscape is a reliable source of information in the environment and expands our understanding of ecological and evolutionary processes. Published in DiRROS: 19.07.2024; Views: 141; Downloads: 141
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648. Virome analysis of signal crayfish (Pacifastacus leniusculus) along its invasion range reveals diverse and divergent RNA virusesKatarina Bačnik, Denis Kutnjak, Silvija Černi, Ana Bielen, Sandra Hudina, 2021, original scientific article Abstract: Crayfish are a keystone species of freshwater ecosystems and a successful invasive species. However, their pathogens, including viruses, remain understudied. The aim of this study was to analyze the virome of the invasive signal crayfish (Pacifastacus leniusculus) and to elucidate the potential differences in viral composition and abundance along its invasion range in the Korana River, Croatia. By the high-throughput sequencing of ribosomal RNA, depleted total RNA isolated from the crayfish hepatopancreas, and subsequent sequence data analysis, we identified novel and divergent RNA viruses, including signal crayfish-associated reo-like, hepe-like, toti-like, and picorna-like viruses, phylogenetically related to viruses previously associated with crustacean hosts. The patterns of reads abundance and calculated nucleotide diversities of the detected viral sequences varied along the invasion range. This could indicate the possible influence of different factors and processes on signal crayfish virome composition: e.g., the differences in signal crayfish population density, the non-random dispersal of host individuals from the core to the invasion fronts, and the transfer of viruses from the native co-occurring and phylogenetically related crayfish species. The study reveals a high, previously undiscovered diversity of divergent RNA viruses associated with signal crayfish, and sets foundations for understanding the potential risk of virus transmissions as a result of this invader’s dispersal. Keywords: signal crayfish virome, RNA viruses, invasive alien species, invasion range, high-throughput sequencing Published in DiRROS: 19.07.2024; Views: 230; Downloads: 112
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649. A chimeric vector for dual use in cyanobacteria and Escherichia coli, tested with cystatin, a nonfluorescent reporter proteinMojca Juteršek, Marko Dolinar, 2021, original scientific article Abstract:
Background
Developing sustainable autotrophic cell factories depends heavily on the availability of robust and well-characterized biological parts. For cyanobacteria, these still lag behind the more advanced E. coli toolkit. In the course of previous protein expression experiments with cyanobacteria, we encountered inconveniences in working with currently available RSF1010-based shuttle plasmids, particularly due to their low biosafety and low yields of recombinant proteins. We also recognized some drawbacks of the commonly used fluorescent reporters, as quantification can be affected by the intrinsic fluorescence of cyanobacteria. To overcome these drawbacks, we envisioned a new chimeric vector and an alternative reporter that could be used in cyanobacterial synthetic biology and tested them in the model cyanobacterium Synechocystis sp. PCC 6803.
Methods
We designed the pMJc01 shuttle plasmid based on the broad host range RSFmob-I replicon. Standard cloning techniques were used for vector construction following the RFC10 synthetic biology standard. The behavior of pMJC01 was tested with selected regulatory elements in E. coli and Synechocystis sp. PCC 6803 for the biosynthesis of the established GFP reporter and of a new reporter protein, cystatin. Cystatin activity was assayed using papain as a cognate target.
Results
With the new vector we observed a significantly higher GFP expression in E. coli and Synechocystis sp. PCC 6803 compared to the commonly used RSF1010-based pPMQAK1. Cystatin, a cysteine protease inhibitor, was successfully expressed with the new vector in both E. coli and Synechocystis sp. PCC 6803. Its expression levels allowed quantification comparable to the standardly used fluorescent reporter GFPmut3b. An important advantage of the new vector is its improved biosafety due to the absence of plasmid regions encoding conjugative transfer components. The broadhost range vector pMJc01 could find application in synthetic biology and biotechnology of cyanobacteria due to its relatively small size, stability and ease of use. In addition, cystatin could be a useful reporter in all cell systems that do not contain papain-type proteases and inhibitors, such as cyanobacteria, and provides an alternative to fluorescent reporters or complements them. Keywords: bacteria, cyanobacteria, synthetic biology, proteolytic cleavage, cystatin Published in DiRROS: 19.07.2024; Views: 108; Downloads: 111
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650. Two new species of parastenocaris (Copepoda, Harpacticoida) from a hyporheic zone and overview of the present knowledge on Stygobiotic Copepoda in Vietnam : historical overview and new dataNgoc-Son Tran, Mau Trinh-Dang, Anton Brancelj, 2021, original scientific article Abstract: The number of freshwater species belonging to the genus Parastenocaris reported from ten countries of Southeast Asia is quite limited. Only two species have been reported so far from freshwater habitats there, compared to over 290 described species of the family Parastenocarididae worldwide. During the first study of the hyporheic zone of two small rivers in central Vietnam, two new species of the family Parastenocarididae were collected, Parastenocaris sontraensis sp. nov. and Parastencaris vugiaensis sp. nov. Both were collected from the gravel bar along the rivers (Suoi Da and Vu Gia river) using the Karaman–Chappuis method. Both the new species belong to the brevipes group of the genus Parastenocaris Kessler, 1913 sensu Lang (1948), and Reid (1995). Parastenocaris sontraensis sp. nov. is similar to P. hinumaensis Kikuchi, 1970 and Parastenocaris jane Karanovic, 2006 in the brevipes-group. Parastenocaris sontraensis sp. nov. differs from both Parastenocaris species by (i) Exp P3 with three segments in the male, (ii) caudal rami with seven setae, and (iii) caudal rami about 2.4 times as long as wide. Parastencaris vugiaensis sp. nov. can be distinguished from its congeners by the unique combination of the following characters: (i) the elliptical shape of caudal rami, (ii) apical seta (V) with bulbous base, and (iii) anal operculum extends beyond the end of anal somite. Until now, 14 stygobiotic species of Copepoda have been recorded in Vietnam (including two new species in this paper), which is relatively few compared with nearby Thailand with 25 species. Short comments on other stygobiotic Copepoda from Vietnam are added. Keywords: Southeast Asia, groundwater fauna, hyporheic zone, Copepoda, new species, taxonomy Published in DiRROS: 19.07.2024; Views: 126; Downloads: 104
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