Fundamental precision limits of fluorescence microscopy: a new perspective on MINFLUX

In the past years, optical fluorescence microscopy (OFM) made steady progress towards increasing the localisation precision of fluorescent emitters in biological samples. The high precision achieved by these techniques has prompted new claims, whose rigorous validation is an outstanding problem. For this purpose, local estimation theory (LET) has emerged as the most used mathematical tool. We establish a novel multi-parameter estimation framework that captures the full complexity of single-emitter localisation in an OFM experiment. Our framework relies on the fact that there are other unknown parameters alongside the emitter's coordinates, such as the average number of photons emitted (brightness), that are correlated to the emitter position, and affect the localisation precision. The increasing complexity of a multi-parameter approach allows for a more accountable assessment of the precision. We showcase our method with MINFLUX microscopy, the OFM approach that nowadays generates images with the best resolution. Introducing the brightness as an unknown parameter, we shed light on features that remain obscure in the conventional approach: the precision can be increased only by increasing the brightness, (i.e., illumination power or exposition time), whereas decreasing the beam separation offers limited advantages. We demonstrate that the proposed framework is a solid and general method for the quantification of single-emitter localisation precision for any OFM approach on equal footing, evaluating the localization precision of stimulated emission depletion (STED) microscopy and making a comparison with MINFLUX microscopy.Comment: 20 pages, 4 figure

Morphology, ultrastructure, and molecular phylogeny of the ciliate Sonderia vorax with insights into the systematics of order Plagiopylida

BACKGROUND: Ciliates of the family Sonderiidae are common members of the eukaryotic communities in various anoxic environments. They host both ecto- and endosymbiotic prokaryotes (the latter associated with hydrogenosomes) and possess peculiar morpho-ultrastructural features, whose functions and homologies are not known. Their phylogenetic relationships with other ciliates are not completely resolved and the available literature, especially concerning electron microscopy and molecular studies, is quite scarce. RESULTS: Sonderia vorax Kahl, 1928 is redescribed from an oxygen-deficient, brackish-water pond along the Ligurian Sea coastlines of Italy. Data on morphology, morphometry, and ultrastructure are reported. S. vorax is ovoid-ellipsoid in shape, dorsoventrally flattened, 130 x 69 μm (mean in vivo); it shows an almost spherical macronucleus, and one relatively large micronucleus. The ventral kinetom has a “secant system” including fronto-ventral and fronto-lateral kineties. A distinctive layer of bacteria laying between kineties covers the ciliate surface. Two types of extrusomes and hydrogenosomes-endosymbiotic bacteria assemblages are present in the cytoplasm. The phylogeny based on 18S rRNA gene sequences places S. vorax among Plagiopylida; Sonderiidae clusters with Plagiopylidae, although lower-level relationships remain uncertain. The studied population is fixed as neotype and the ciliate is established as type species of the genus, currently lacking. CONCLUSIONS: This is the first description of a representative of Sonderiidae performed with both morphological and molecular data. To sum up, many previous hypotheses on this interesting, poorly known taxon are confirmed but confusion and contradictory data are as well highlighted

Resistance and resilience of ecosystem descriptors and properties to dystrophic events: a study case in a Mediterranean lagoon

Mediterranean lagoons are naturally exposed, during the dry season, to dystrophic and hypoxic events determining dis-equilibrium conditions along temporal and spatial scales, which are linked to metabolism and life cycle of the biotic components. In summer 2008, Lesina lagoon (SE Italian coastline) was interested by a geographically localized dystrophic crisis which affected up to 8% of the total lagoon surface. Temporal dynamics of principal descriptors of abiotic (water, sediment) and biotic (phytoplankton, benthic macroinvertebrate) compartments have been followed during the 2008 by collecting data inside stressed and control lagoon areas before a dystrophic event and in the six months after the dystrophic event. The aim of the study was to analyse the pathways of ecosystem responses to dystrophic stress, searching for the characteristic scales of ecosystem compartment resistance and resilience. The characteristic time-scale of abiotic and biotic component time responses varied from days, for the selected markers of the water column, to year, for the benthic ones. Short-term biotic and abiotic responses in the water column were strongly coupled while biotic and abiotic responses at the sediment level were remarkably un-coupled. Dynamics and recovery time of water column and benthic components do not match in Lesina following the dystrophic crisis, highlighting an intrinsic individualistic behavior within the lagoon community driving ecosystem processes and ecosystem level responses. Taxonomic and non-taxonomic descriptors of both phytoplankton and benthic macroinvertebrates showed different response patterns as early warning signals and overall resilience. The emphasized differences in the stability components, i.e., resistance and resilience, of water column and sediment abiotic and biotic characteristics as well as of taxonomic and non-taxonomic descriptors has key implication in planning monitoring strategies and programs for transitional waters in the Mediterranean and Black Sea EcoRegions

Effects of environmental cocaine concentrations on COX and caspase-3 activity, GRP-78, ALT, CRP and blood glucose levels in the liver and kidney of the European eel (Anguilla anguilla)

Abstract Cocaine is one of the most widely used illicit drugs in the world, and as a result of incomplete removal by sewage treatment plants it is found in surface waters, where it represents a new potential risk for aquatic organisms. In this study we evaluated the influence of environmental concentrations of cocaine on the liver and the kidney of the European eel (Anguilla anguilla). The eels were exposed to 20 ng L−1 of cocaine for fifty days, after which, three and ten days after the interruption of cocaine exposure their livers and kidneys were compared to controls. The general morphology of the two organs was evaluated, as well as the following parameters: cytochrome oxidase (COX) and caspase-3 activities, as markers of oxidative metabolism and apoptosis activation, respectively; glucose-regulated protein (GRP)78 levels, as a marker of endoplasmic reticulum (ER)-stress; blood glucose level, as stress marker; serum levels of alanine aminotransferase (ALT), as a marker of liver injury and serum levels of C-reactive protein (CRP), as a marker of the inflammatory process. The liver showed morphologic alterations such as necrotic areas, karyolysis and pyknotic nuclei, while the kidneys had dilated glomeruli and the renal tubules showed pyknotic nuclei and karyolysis. In the kidney, the alterations persisted after the interruption of cocaine exposure. In the liver, COX and caspase-3 activities increased (COX: P = 0.01; caspase-3: P = 0.032); ten days after the interruption of cocaine exposure, COX activity returned to control levels (P = 0.06) whereas caspase-3 activity decreased further (P = 0.012); GRP78 expression increased only in post-exposure recovery specimens (three days: P = 0.007 and ten days: P = 0.008 after the interruption of cocaine exposure, respectively). In the kidney, COX and caspase-3 activities increased (COX: P = 0.02; caspase-3: P = 0.019); after the interruption of cocaine exposure, COX activity remained high (three days: P = 0.02 and ten days: P = 0.029 after the interruption of cocaine exposure, respectively) whereas caspase-3 activity returned to control values (three days: P = 0.69 and ten days: P = 0.67 after the interruption of cocaine exposure, respectively). Blood glucose and serum ALT and CRP levels increased (blood glucose: P = 0.01; ALT: P = 0.001; CRP: 0.015) and remained high also ten days after the interruption of cocaine exposure (blood glucose: P = 0.009; ALT: P = 0.0031; CRP: 0.036). These results suggest that environmental cocaine concentrations adversely affected liver and kidney of this species

An individual-based dataset of carbon and nitrogen isotopic data of Callinectes sapidus in invaded Mediterranean waters

[EN] Background The characterisation of functional traits of non-indigenous and invasive species is crucial to assess their impact within invaded habitats. Successful biological invasions are often facilitated by the generalist diet of the invaders which can modify their trophic position and adapt to new ecosystems determining changes in their structure and functioning. Invasive crustaceans are an illustrative example of such mechanisms since their trophic habits can determine important ecological impacts on aquatic food webs. The Atlantic blue crab Callinectes sapidus is currently established and considered invasive in the Mediterranean Sea where it has been recorded for the first time between 1947 and 1949. In the last decade, the blue crab colonised most of the eastern and central Mediterranean Sea and the Black Sea and it is currently widening its distribution towards the western region of the basin. New information Stable isotope analysis is increasingly used to investigate the trophic habits of invasive marine species. Here, we collated individual measures of the blue crab d C and d N values and of its potential invertebrate prey into a geo-referenced dataset. The dataset includes 360 records with 236 isotopic values of the blue crab and 224 isotopic data of potential prey collected from five countries and 12 locations between 2014 and 2019. This dataset allows the estimation of the trophic position of the blue crab within a variety of invaded ecosystems, as well as advanced quantitative comparisons of the main features of its isotopic niche.Di Muri, C.; Rosati, I.; Bardelli, R.; Cilenti, L.; Veli, DL.; Falco, S.; Vizzini, S.... (2022). An individual-based dataset of carbon and nitrogen isotopic data of Callinectes sapidus in invaded Mediterranean waters. Biodiversity Data Journal (Online). 10:1-12. https://doi.org/10.3897/BDJ.10.e775161121

Towards Semantic Data Management in LifeWatch Italy: the Phytoplankton Study Case

LifeWatch Italy, the Italian node of LifeWatch-ERIC, has promoted and stimulated the debate on the use of semantic in the biodiversity data management. Actually, information from biodiversity and ecosystems is very heterogeneous and needs to be better managed in order to improve the actual scientific knowledge, as well as to address the urgent societal challenges concerning environmental issues. Here we present the Phytoplankton Study Case, where the semantic approach was used to address data harmonisation, integration and discovery. An interdisciplinary team of LifeWatch Italy has developed a thesaurus on phytoplankton functional traits and linked its concepts to other existing conceptual schema related to the specific domain. In the meantime, the team has produced the LifeWatch Core Ontology, a customization of the OBOE core ontology, for the semantic description/capture of basic concepts and relationships in ecological studies. This framework ontology is based on 7 main concepts (classes) as Domain, Entity, Observation, Characteristic, Measurement, Protocol, Standard, providing a structured yet generic approach for semantic data annotation, and for developing domain-specific ecological ontologies as the Phytoplankton Trait Ontology (PhyTO). To date, LifeWatch e-Infrastructure stores and manages data and metadata using an mix of Database Management Systems (the Relational MySQL and the NoSQL MONGO DB); for the purpose of the study case, we selected the VIRTUOSO Triple Store as semantic repository and we developed different modules to automate the management workflow. A first software module has been developed to allow the data annotation with classes, subclasses and properties of the PhyTO (i.e. Semantic Annotation). The designed module allows to map metadata and data stored in the LifeWatch Data Portal with the OWL schema of the PhyTO and to produce .rdf output files. A second developed module uses as input the .rdf files and store the data in the VIRTUOSO Graph to make them available for the semantic search. Moreover, a user-friendly search interface (i.e. Java Portlet) has been implemented to retrieve annotated data with queries suggested by the data users. This approach facilitates data discovery and integration, and can provide guidance for, and automate, data aggregation and summary

Patterns of functional diversity of macroinvertebrates across three aquatic ecosystem types, NE Mediterranean

This study is focused on investigating the variation patterns of macroinvertebrate guilds functional structure, in relation to the taxonomic one, across aquatic ecosystem types along the salinity gradient from freshwater to marine and the resulting implications on guild organization and energy flows. Synoptic samplings have been carried out using the leaf-pack technique at 30 sites of the aquatic ecosystems of the Corfu Island (Greece), including freshwater, lagoon, and marine sites. Here, we analyzed the macroinvertebrate guilds of river, lagoon, and marine ecosystems, as: i. taxonomic composition and population abundance ii. trophic guilds composition and relative abundance; and iii. body size spectra and size patterns. The following variation patterns across the three ecosystem types were observed: a. trophic guild composition and body size spectra were more conservative than taxonomic composition within and among ecosystem types, where, trophic guild and size spectra composition were more similar between river and lagoon ecosystem types than with marine ones; b. a dominance on resource exploitation of large species over smaller ones was inferred at all sites; and, c. higher body size-specific density of individuals was consistently observed in lagoon than in freshwater and marine ecosystems. Results extend previous findings suggesting a common hierarchical organization of benthic macroinvertebrate guilds in aquatic ecosystems and showing that lagoon ecosystems have higher energy density transferred to benthic macroinvertebrates than both freshwater and marine ecosystem types

How much biodiversity is concealed in the word ‘biodiversity’?

Non peer reviewe