BioEncoder: A metric learning toolkit for comparative organismal biology.

In the realm of biological image analysis, deep learning (DL) has become a core toolkit, for example for segmentation and classification. However, conventional DL methods are challenged by large biodiversity datasets characterized by unbalanced classes and hard-to-distinguish phenotypic differences between them. Here we present BioEncoder, a user-friendly toolkit for metric learning, which overcomes these challenges by focussing on learning relationships between individual data points rather than on the separability of classes. BioEncoder is released as a Python package, created for ease of use and flexibility across diverse datasets. It features taxon-agnostic data loaders, custom augmentation options, and simple hyperparameter adjustments through text-based configuration files. The toolkit's significance lies in its potential to unlock new research avenues in biological image analysis while democratizing access to advanced deep metric learning techniques. BioEncoder focuses on the urgent need for toolkits bridging the gap between complex DL pipelines and practical applications in biological research.

Trait-Fitness Associations via Fecundity and Competition in a Two-Million-Year-Long Fossil Record.

AbstractThe evolution of phenotypic traits is usually studied on generational timescales or across species on million-year timescales. We bridge this conceptual gap by using high-density sampling of a species lineage, Microporella agonistes (Bryozoa, Cheilostomatida), over 2 million years of its evolutionary history, to ask whether trait-fitness associations are consistent with evolutionary trait models often applied to phenotypic time series. We use average fecundity and competitive outcome as two different fitness components, where competitive outcome is a proxy for partial survival. Examining three quantitative traits in multivariate analyses, we present evidence that some traits experienced substantial selective pressures, in part controlled by past environments. A complex interplay of resource competition with an altering set of competitors and past temperatures has contributed to the changing patterns of phenotypes within the focal species. A comparison with congeneric species living in the same regional community suggests that size traits are more temporally variable and less constrained than shape traits. Our analyses also show that while controls on phenotypes are complex and varied in time, ecological and evolutionary processes that unfold on shorter timescales are not inconsistent with macroevolutionary patterns observed on longer timescales.

Qualitative Metabolite Profiling of Orchis purpurea Huds. by GC and UHPLC/MS Approaches.

Orchids are experiencing wide success in ornamental, medicinal, and food fields. The reason for their success is correlated with both their morphology and metabolomics, the latter linked to their taste and biological effects. Despite many orchids having already been the subject of chemotaxonomic works, some of them are still untapped, like the case of Orchis purpurea. O. purpurea is one of the most common species of the genus Orchis, present in hedgerows, verges, and light woodland, where it is one of the few herbaceous plants able to be unpleasant to herbivorous animals. Essential oil from roots, stems, leaves, and flowers were analyzed via GC/MS analyses, revealing the presence of 70 compounds, with a clear prevalence of coumarin. The high concentration of this metabolite may explain the resistance of O. purpurea to herbivores, being associated with appetite-suppressing properties and a bitter taste. Non-volatile fractions were analyzed via UHPLC-MS analysis revealing the presence of hydroxycinnamic acid derivatives, polyphenols, and glycosidic compounds, probably responsible for their color and fragrance. Taken together, the herein presented results shed light on both the defensive strategy and the chemotaxonomy of O. purpurea.

Neurodegeneration: can metabolites from Eremurus persicus help?

The number of patients affected by neurodegenerative diseases is increasing worldwide, and no effective treatments have been developed yet. Although precision medicine could represent a powerful tool, it remains a challenge due to the high variability among patients. To identify molecules acting with innovative mechanisms of action, we performed a computational investigation using SAFAN technology, focusing specifically on HuD. This target belongs to the human embryonic lethal abnormal visual-like (ELAV) proteins and plays a key role in neuronal plasticity and differentiation. The results highlighted that the molecule able to bind the selected target was (R)-aloesaponol-III-8-methyl ether [(R)-ASME], a metabolite extracted from Eremurus persicus. Notably, this molecule is a TNF-α inhibitor, a cytokine involved in neuroinflammation. To obtain a suitable amount of (R)-ASME to confirm its activity on HuD, we optimized the extraction procedure. Together with ASME, another related metabolite, germichrysone, was isolated. Both ASME and germichrysone underwent biological investigation, but only ASME confirmed its ability to bind HuD. Given the multifactorial nature of neurodegenerative diseases, we decided to investigate ASME as a proteasome activator, being molecules endowed with this kind of activity potentially able to counteract aggregations of dysregulated proteins. ASME was able to activate the considered target both in enzymatic and cellular assays. Therefore, ASME may be considered a promising hit in the fight against neurodegenerative diseases.

Teodorico Borgognoni's Formulary for Thirteenth Century Anesthetic Preparations.

Teodorico Borgognoni was born in Lucca in 1205 and was appointed bishop of Bitonto and Cervia in 1262 and 1270. Following his father, he learned the art of surgery and collected relevant recipes in his most important work, entitled Cyrurgia seu filia principis. Among the disciplines reported in this work, the most interesting and innovative is anesthesia. The recipes in this field contribute to Borbognoni's consideration as the forerunner of modern anesthesia. Such recipes have been reported in other manuscripts from the Middle Ages, like Manuscript No. 1939. In the present work, we investigate the traditional preparations handed down in this manuscript, focusing on type of preparation and botanical ingredients. The results highlight that exploited ingredients can be divided into three groups: the first comprises plants already known for their narcotic effects, the second includes ingredients acting as an adjuvant for absorption or reducing the metabolism, and the last group includes ingredients not associated with biological activity to explain their presence in anesthetic recipes. This third group is of particular interest for future biological investigations. Our goal is to rekindle attention to the work of Teodorico Borgognoni on traditional preparation for anesthetic purposes: a topic often underestimated by ethnobotanical surveys.

Increasing risk of invasions by organisms on marine debris in the Southeast coast of India.

Increasing amount of anthropogenic litter in the marine environment has provided an enormous number of substrates for a wide range of marine organisms, thus serving as a potential vector for the transport of fouling organisms. Here, we examined the fouling organisms on different types of stranded litter (plastic, glass, rubber, foam sponge, cloth, metal and wood) on eight beaches along the southeast coast of India. In total, 17 encrusting species belonging to seven phyla (Arthropoda, Bryozoa, Mollusca, Annelida, Cnidaria, Chlorophyta and Foraminifera) were identified on 367 items, with one invasive species, the mussel Mytella strigata, detected. The most common species associated with marine litter were the cosmopolitan bryozoans Jellyella tuberculata (%O = 31.64 %) and J. eburnea (28.61 %), the barnacle species Lepas anserifera (29.97 %), Amphibalanus amphitrite (22.34 %) and Amphibalanus sp. (14.16 %), and the oyster species Saccostrea cucullata (13.62 %) and Magallana bilineata (5.44 %). We also reported the first records on stranded litter of four species: the gastropod species Pirenella cingulata and Umbonium vestiarium, the foraminiferan Ammonia beccarii, and the oyster M. bilineata. This study is thus the first documentation of marine litter as a vector for species dispersal in India, where the production and consumption of plastic rank among the highest in the world. We also highlight the increasing risk of invasions by non-indigenous organisms attached to debris along the southeast coast of India. Comprehensive monitoring efforts are thus needed to elucidate the type of vectors responsible for the arrival of invasive species in this region. Raising awareness and promoting education are vital components in fostering sustainable solutions to combat plastic pollution in the country and globally.

Structural Insights into the Ligand-LsrK Kinase Binding Mode: A Step Forward in the Discovery of Novel Antimicrobial Agents.

LsrK is a bacterial kinase that triggers the quorum sensing, and it represents a druggable target for the identification of new agents for fighting antimicrobial resistance. Herein, we exploited tryptophan fluorescence spectroscopy (TFS) as a suitable technique for the identification of potential LsrK ligands from an in-house library of chemicals comprising synthetic compounds as well as secondary metabolites. Three secondary metabolites (Hib-ester, Hib-carbaldehyde and (R)-ASME) showed effective binding to LsrK, with KD values in the sub-micromolar range. The conformational changes were confirmed via circular dichroism and molecular docking results further validated the findings and displayed the specific mode of interaction. The activity of the identified compounds on the biofilm formation by some Staphylococcus spp. was investigated. Hib-carbaldehyde and (R)-ASME were able to reduce the production of biofilm, with (R)-ASME resulting in the most effective compound with an EC50 of 14 mg/well. The successful application of TFS highlights its usefulness in searching for promising LsrK inhibitor candidates with inhibitor efficacy against biofilm formation.

Scanning electron microscopy study of Lars Silns cheilostome bryozoan type specimens in the historical collections of natural history museums in Sweden.

The type specimens of 42 cheilostome bryozoan species introduced by Lars Siln between 1938 and 1954 and housed at three different Swedish institutions (the Swedish Museum of Natural History in Stockholm, the Biological Museum in Lund and the Museum of Evolution in Uppsala) are here revised using scanning electron microscopy, with two exceptions, for the first time. As a result of this revision, new morphological observations were made for some species, such as ooecia in Antropora erecta, a costal pseudopore in Jullienula hippocrepis, intracolonial variation in the number of intracostal windows in Costaticella gisleni, and oral spines in Triphyllozoon mauritzoni. Some other observations confirmed the presence of structures/polymorphs in type material that had previously only been noted in non-type specimens, such as spinose interzooidal kenozooids in Retevirgula triangulata and putative brooding zooids in Bugulina kiuschiuensis. Structures originally interpreted as hydroid tube openings on the dorsal side of Triphyllozoon microstigmatum were confirmed to be avicularia, while the supposed kenozooidal attachment rootlet of Fedora nodosa might be the polypide tube of a coronate scyphozoan. In addition, the original combination Heliodoma goesi is here reinstated after Lagaaij assigned the species to Setosellina in 1963. The following new combinations are also proposed: Labioporella aviculifera for Siphonoporella aviculifera; Mangana canui and Mangana incrustata for Callopora canui and Tegella incrustata, respectively; Sphaerulobryozoon ovum for Fedora ovum. Lectotypes were selected when appropriate. This work clarifies the exact identity of some species that have never been recorded after their first description, such as Stylopoma magnovicellata and three species of Triphyllozoon, and contributes to the current increasing effort to digitize historical key specimens in natural history museum collections.

Walking around the Autonomous Province of Trento (Italy): An Ethnobotanical Investigation.

The Trentino-South Tyrol region is a special statute region of northeastern Italy. This territory is of particular interest for its morphology, flourishing vegetation, and history, having been a meeting area among different civilizations. Hence, Trentino is characterized by an ethnic plurality and a rich ethnobotanical knowledge, even if the available information is fragmentary, widely dispersed, and often guarded in oral popular culture. To fill this gap, in the present work 200 subjects were interviewed using an ethnobotanical survey. The resulting 817 citations referred to 64 native species, used either for human or animal health or for domestic purposes. As a second step, for each plant exploited for medicinal purposes, local importance was evaluated by calculating their relative frequency of citation. Moreover, the main traditional preparations were discussed. Among them, the most cited and exploited ones are Achillea millefolium, Arnica montana, Hypericum perforatum, Malva sylvestris, Pinus mugo, and Satureja montana, for which a deeper analysis has been performed. Lastly, the ethnobotanical knowledge of the plants growing in this territory will add a piece to the mosaic of traditional medicine in Italy and may lay the foundation for a nature-aided drug discovery process.

Revision of the type species of some cheilostome bryozoan genera in the collection of the Swedish Museum of Natural History.

The zoological dry collection of the Swedish Museum of Natural History in Stockholm includes an important, historical bryozoan section that is rich in species and specimens and also diverse from a geographical point of view. This collection also contains the type specimens of the type species of some cheilostome bryozoan genera introduced by several naturalists and bryozoologists between the mid-1800s and 1900s. With a few exceptions, these have not been revised since the advent of scanning electron microscopy as a standard tool for bryozoan taxonomy. Here, the type specimen(s) of the type species of the following six cheilostome genera are described and illustrated using SEM micrographs for the first time: Cheilopora Levinsen, 1909; Fedorella Siln, 1947; Floridina Jullien, 1882; Lepraliella Levinsen, 1917; Smittipora Jullien, 1882; and Stenopsella Bassler, 1952. The type specimen(s) of the type species of the recently introduced Terwasipora Reverter-Gil Souto, 2019 and the relatively recently revised Doryporella Norman, 1903 are also illustrated for the first time. This revision has identified some erroneous geographical records for some of the species/genera examined, and has led to the proposed synonymy of Stenopsella with Gigantopora Ridley, 1881. Lectotypes have also been selected. All of the images produced will also be publicly available through the SMNH online catalogue. The digitisation of natural history museum collections, with prioritisation of historical type specimens, is of paramount importance to facilitate access to the fundamental taxonomic units for scientists worldwide.

Changing allometric relationships among fossil and Recent populations in two colonial species.

Allometry is vital for understanding the mechanisms underlying phenotypic evolution. Despite a large body of literature on allometry, studies based on fossil time series are limited for solitary organisms and nonexistent for colonial organisms. Allometric relationships have been found to be relatively constant across Recent populations of the same species, separated by space, but variable among fossil populations separated by thousands of years. How stable are allometric relationships at the module level for colonial organisms? We address this question using two extant species of the cheilostome bryozoan Microporella with fossil records spanning the Pleistocene of New Zealand. We investigate size covariation between feeding modules and three traits with separate functions (reproductive, resource uptake, and defense). We found that within-population (static) allometry can change on timescales of at least 0.1 million years. These within-population relationships do not consistently predict overintraspecific evolutionary allometry, which in turn does not predict those estimated at the genus level. Different functional traits are constrained to different extents by module size with defensive traits being the least constrained and most evolvable, compared with reproductive and resource uptake traits. Our study highlights the potential of colonial organisms in understanding the constraints and drivers of long-term phenotypic change.

Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny.

Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.

Marine biofouling organisms on beached, buoyant and benthic plastic debris in the Catalan Sea.

Plastic debris provides long-lasting substrates for benthic organisms, thus acting as a potential vector for their dispersion. Its interaction with these colonizers is, however, still poorly known. This study examines fouling communities on beached, buoyant and benthic plastic debris in the Catalan Sea (NW Mediterranean), and characterizes the plastic type. We found 14 specimens belonging to two phyla (Annelida and Foraminifera) on microplastics, and more than 400 specimens belonging to 26 species in 10 phyla (Annelida, Arthropoda, Brachiopoda, Bryozoa, Chordata, Cnidaria, Echinodermata, Mollusca, Porifera and Sipuncula) on macroplastics. With 15 species, bryozoans are the most diverse group on plastics. We also report 17 egg cases of the catshark Scyliorhinus sp., and highlight the implications for their dispersal. Our results suggest that plastic polymers may be relevant for distinct fouling communities, likely due to their chemical structure and/or surface properties. Our study provides evidence that biofouling may play a role in the sinking of plastic debris, as the most abundant fouled plastics had lower densities than seawater, and all bryozoan species were characteristic of shallower depths than those sampled. More studies at low taxonomic level are needed in order to detect new species introduction and potential invasive species associated with plastic debris.

New insight into pectin effects on mesophyll conductance in four species of deciduous Forest.

The amount of pectin in the cell wall is considered a critical element regulating cell wall porosity. Thus, it is likely to influence the diffusional processes particularly that from the substomatal cavities to the carboxylation sites in the chloroplast stroma (i.e. mesophyll conductance, gm). We analyzed in four deciduous species (Acer campestre, Crateaugus monogyna, Corylus avellana, Quercus robur) the correlation between pectin and gm in two phase of leaves development (i.e. mature green leaves and senescent leaves). Results showed that in A. campestre, C. monogyna and Q. robur to higher value of pectin in mature green leaves corresponded the higher gm value. Taking into account this result, we can assume that a higher amount of pectins is associated to an increased cell wall hydrophilicity and elasticity, thus increasing gm because CO2 molecules cross the wall dissolved in water. An opposite behavior was observed in C. avellana.

Anti-Multiple Myeloma Potential of Secondary Metabolites from Hibiscus sabdariffa-Part 2.

Multiple Myeloma (MM) is an aggressive tumor causing millions of deaths every year and currently available therapies are often unsuccessful or correlated with severe side effects. In our previous work we demonstrated that the Hibiscus sabdariffa hydroalcoholic extract inhibits the growth of the MM cell line and we isolated two metabolites responsible for the activity: Hib-ester and Hib-carbaldehyde. Herein we report their interaction with proteasome, one of the main targets in the fight against MM. The molecular modelling study outlined a good interaction of both compounds with the target and these results prompted us to investigate their potential to inhibit proteasome. Metabolites were then isolated from the calyces and an extract with a high content of Hib-ester and Hib-carbaldehyde was prepared. An anticancer profile was drawn, evaluating apoptosis, autophagy and proteasome inhibition, with the anticancer properties being mainly attributed to the Hib-ester and Hib-carbaldehyde, while the proteasome inhibition of the extract could also be ascribed to the presence of anthocyanins, a class of secondary metabolites already known for their proteasome inhibitory activity.

When fossil clades 'compete': local dominance, global diversification dynamics and causation.

Examining the supposition that local-scale competition drives macroevolutionary patterns has become a familiar goal in fossil biodiversity studies. However, it is an elusive goal, hampered by inadequate confirmation of ecological equivalence and interactive processes between clades, patchy sampling, few comparative analyses of local species assemblages over long geological intervals, and a dearth of appropriate statistical tools. We address these concerns by reevaluating one of the classic examples of clade displacement in the fossil record, in which cheilostome bryozoans surpass the once dominant cyclostomes. Here, we analyse a newly expanded and vetted compilation of 40 190 fossil species occurrences to estimate cheilostome and cyclostome patterns of species proportions within assemblages, global genus richness and genus origination and extinction rates while accounting for sampling. Comparison of time-series models using linear stochastic differential equations suggests that inter-clade genus origination and extinction rates are causally linked to each other in a complex feedback relationship rather than by simple correlations or unidirectional relationships, and that these rates are not causally linked to changing within-assemblage proportions of cheilostome versus cyclostome species.

Seek and ye shall find: new species and new records of Microporella (Bryozoa, Cheilostomatida) in the Mediterranean.

The Mediterranean specimens of the genus Microporella collected from shallow water habitats during several surveys and cruises undertaken mostly off the Italian coast are revised. As a result of the disentanglement of the M.ciliata complex and the examination of new material, three new species, M.bicollaris sp. nov., M.ichnusae sp. nov., and M.pachyspina sp. nov., are described from submarine caves or associated with seagrasses and algae. An additional species Microporella sp. A, distinct by its finely reticulate ascopore, is described but left in open nomenclature owing to the limitations of a single infertile fragment. After examination of all available material, based on their identical zooidal morphology, the genus Diporula is regarded as junior synonym of Microporella and the combination Microporellaverrucosa is resurrected as first suggested by Neviani in 1896. Fenestrulinajoannae is also reassigned to Microporella. The availability of a large number of colonies of the above-mentioned and other species already well known from the area (i.e., M.appendiculata, M.ciliata, and M.modesta), allowed the assessment of their high intraspecific variability as well as the observation, for the first time, of some morphological characters including ancestrulae, early astogeny, and kenozooids. Finally, M.modesta, in spite of M.ciliata as defined by the neotype selected by Kuklinski & Taylor in 2008, appears to be the commonest species in the basin.

A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group.

Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air-dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.

Microwave-Assisted Extraction and HPLC-UV-CD Determination of (S)-usnic Acid in Cladonia foliacea.

During the years, many usnic acid (UA) conjugates have been synthesized to obtain potent endowed with biological properties. Since (S)-UA is less abundant in nature than (R)-enantiomer, it is difficult to source, thus precluding a deeper investigation. Among the lichens producing UA, Cladonia foliacea is a valuable (S)-UA source. In the present work, we report on a rapid HPLC-UV/PAD-CD protocol suitable for the analysis and the identification of the main secondary metabolites present in C. foliacea extract. Best results were achieved using XBridge Phenyl column and acetonitrile and water, which were both added with formic acid as mobile phase in gradient elution. By combining analytical, spectroscopical, and chiroptical analysis, the most abundant analyte was unambiguously identified as (S)-UA. Accordingly, a versatile microwave-assisted extractive (MAE) protocol, assisted by a design of experiment (DoE), to quantitatively recover (S)-UA was set up. The best result in terms of UA extraction yield was obtained using ethanol and heating at 80 °C under microwave irradiation for 5 min. Starting from 100 g of dried C. foliacea, 420 mg of (S)-UA were achieved. Thus, our extraction method resulted in a suitable protocol to produce (S)-UA from C. foliacea for biological and pharmaceutical investigation or commercial purposes.

Trait-fitness associations do not predict within-species phenotypic evolution over 2 million years.

Long-term patterns of phenotypic change are the cumulative results of tens of thousands to millions of years of evolution. Yet, empirical and theoretical studies of phenotypic selection are largely based on contemporary populations. The challenges in studying phenotypic evolution, in particular trait-fitness associations in the deep past, are barriers to linking micro- and macroevolution. Here, we capitalize on the unique opportunity offered by a marine colonial organism commonly preserved in the fossil record to investigate trait-fitness associations over 2 Myr. We use the density of female polymorphs in colonies of Antartothoa tongima as a proxy for fecundity, a fitness component, and investigate multivariate signals of trait-fitness associations in six time intervals on the backdrop of Pleistocene climatic shifts. We detect negative trait-fitness associations for feeding polymorph (autozooid) sizes, positive associations for autozooid shape but no particular relationship between fecundity and brood chamber size. In addition, we demonstrate that long-term trait patterns are explained by palaeoclimate (as approximated by ∂18O), and to a lesser extent by ecological interactions (i.e. overgrowth competition and substrate crowding). Our analyses show that macroevolutionary outcomes of trait evolution are not a simple scaling-up from the trait-fitness associations.