Assemblage Structure of Ichthyoplankton Communities in the Southern Adriatic Sea (Eastern Mediterranean).

Studies based on fish early life stages can provide information on spawning grounds and nursery areas, helping to determine the implications for stock biomass fluctuations of recruitment variability. This study describes the composition, abundance, spatial distribution and differences in day/night vertical distribution of ichthyoplankton in the southern Adriatic Sea. Samples were collected within the framework of the COCONET project (Towards COast to COast NETworks of marine protected areas) from 9 to 18 May 2013 by the R/V Urania, using the electronic multinet EZ-NET BIONESS (Bedford Institute of Oceanography Net Environmental Sampling System). A total of 20 species, belonging to 20 genera and 13 families, were identified. Of the collected larvae, 74.3% were meso- or bathypelagic species, 24.7% were epipelagic and 0.9% were demersal. The community was dominated by Gonostomatidae, followed by Engraulidae, Myctophidae and Photychthaidae. The most abundant species was Cyclothone braueri (45.6%), followed by Engraulis encrasicolus, Ceratoscopelus maderensis, Cyclothone pygmaea, Vinciguerria attenuata and Myctophum punctatum. An inshore/offshore increasing gradient in biodiversity and abundance was observed. Different weighted mean depths (WMDs) were observed for larvae and juveniles. No diel vertical migrations were observed. The high abundance of meso- or bathypelagic species in the upper 100 m confirms the epipelagic zone as an important environment for the development of the larval stages of these fish.

BAFF and APRIL counterregulate susceptibility to inflammation-induced preterm birth.

Clinical evidence points to a function for B cell-activating factor (BAFF) in pregnancy. However, direct roles for BAFF-axis members in pregnancy have not been examined. Here, via utility of genetically modified mice, we report that BAFF promotes inflammatory responsiveness and increases susceptibility to inflammation-induced preterm birth (PTB). In contrast, we show that the closely related A proliferation-inducing ligand (APRIL) decreases inflammatory responsiveness and susceptibility to PTB. Known BAFF-axis receptors serve a redundant function in signaling BAFF/APRIL presence in pregnancy. Treatment with anti-BAFF/APRIL monoclonal antibodies or BAFF/APRIL recombinant proteins is sufficient to manipulate susceptibility to PTB. Notably, macrophages at the maternal-fetal interface produce BAFF, while BAFF and APRIL presence divergently shape macrophage gene expression and inflammatory function. Overall, our findings demonstrate that BAFF and APRIL play divergent inflammatory roles in pregnancy and provide therapeutic targets for mitigating risk of inflammation-induced PTB.

B cell-activating factor (BAFF) from dendritic cells, monocytes and neutrophils is required for B cell maturation and autoantibody production in SLE-like autoimmune disease.

Purpose and methods: B cell-activating factor (BAFF) contributes to the pathogenesis of autoimmune diseases including systemic lupus erythematosus (SLE). Although several anti-BAFF Abs and derivatives have been developed for the treatment of SLE, the specific sources of BAFF that sustain autoantibody (auto-Ab) producing cells have not been definitively identified. Using BAFF-RFP reporter mice, we identified major changes in BAFF-producing cells in two mouse spontaneous lupus models (Tlr7 Tg mice and Sle1), and in a pristane-induced lupus (PIL) model. Results: First, we confirmed that similar to their wildtype Tlr7 Tg and Sle1 mice counterparts, BAFF-RFP Tlr7 Tg mice and BAFF-RFP Sle1 mice had increased BAFF serum levels, which correlated with increases in plasma cells and auto-Ab production. Next, using the RFP reporter, we defined which cells had dysregulated BAFF production. BAFF-producing neutrophils (Nphs), monocytes (MOs), cDCs, T cells and B cells were all expanded in the spleens of BAFF-RFP Tlr7 Tg mice and BAFF-RFP Sle1 mice compared to controls. Furthermore, Ly6Chi inflammatory MOs and T cells had significantly increased BAFF expression per cell in both spontaneous lupus models, while CD8- DCs up-regulated BAFF expression only in the Tlr7 Tg mice. Similarly, pristane injection of BAFF-RFP mice induced increases in serum BAFF levels, auto-Abs, and the expansion of BAFF-producing Nphs, MOs, and DCs in both the spleen and peritoneal cavity. BAFF expression in MOs and DCs, in contrast to BAFF from Nphs, was required to maintain homeostatic and pristane-induced systemic BAFF levels and to sustain mature B cell pools in spleens and BMs. Although acting through different mechanisms, Nph, MO and DC sources of BAFF were each required for the development of auto-Abs in PIL mice. Conclusions: Our findings underscore the importance of considering the relative roles of specific myeloid BAFF sources and B cell niches when developing treatments for SLE and other BAFF-associated autoimmune diseases.

NO and Heme Proteins: Cross-Talk between Heme and Cysteine Residues.

Heme proteins are a diverse group that includes several unrelated families. Their biological function is mainly associated with the reactivity of the heme group, which-among several other reactions-can bind to and react with nitric oxide (NO) and other nitrogen compounds for their production, scavenging, and transport. The S-nitrosylation of cysteine residues, which also results from the reaction with NO and other nitrogen compounds, is a post-translational modification regulating protein activity, with direct effects on a variety of signaling pathways. Heme proteins are unique in exhibiting this dual reactivity toward NO, with reported examples of cross-reactivity between the heme and cysteine residues within the same protein. In this work, we review the literature on this interplay, with particular emphasis on heme proteins in which heme-dependent nitrosylation has been reported and those for which both heme nitrosylation and S-nitrosylation have been associated with biological functions.

WHO Laboratory Biosafety Manual: A New Approach to Security.

The paper aims to highlight the new indications introduced in the 4th edition of the "Laboratory Biosafety Manual" of World Health Organization. The authors propose a new vision to improve biosafety and biosecurity in the laboratory aligned with the technical standards ISO 35001:2019 "Biorisk management for laboratories and other related organizations" and ISO 45001:2018 "Occupational health and safety management systems-Requirements with guidelines for use" framework. The current edition has a more innovative approach compared to the previous ones, more attention is given to training awareness and providing skills, to promote the culture of safety by adopting an approach based on risk analysis, rather than the prescriptive approach that has been used previously.

The Evolution of Nitric Oxide Function: From Reactivity in the Prebiotic Earth to Examples of Biological Roles and Therapeutic Applications.

Nitric oxide was once considered to be of marginal interest to the biological sciences and medicine; however, there is now wide recognition, but not yet a comprehensive understanding, of its functions and effects. NO is a reactive, toxic free radical with numerous biological targets, especially metal ions. However, NO and its reaction products also play key roles as reductant and oxidant in biological redox processes, in signal transduction, immunity and infection, as well as other roles. Consequently, it can be sensed, metabolized and modified in biological systems. Here, we present a brief overview of the chemistry and biology of NO-in particular, its origins in geological time and in contemporary biology, its toxic consequences and its critical biological functions. Given that NO, with its intrinsic reactivity, appeared in the early Earth's atmosphere before the evolution of complex lifeforms, we speculate that the potential for toxicity preceded biological function. To examine this hypothesis, we consider the nature of non-biological and biological targets of NO, the evolution of biological mechanisms for NO detoxification, and how living organisms generate this multifunctional gas.

Expression of Recombinant Cold-Adapted (Hemo)Globins from Marine Bacteria.

The production of recombinant proteins in bacteria made possible to obtain large quantities of proteins essential for basic and applied research. Escherichia coli remains one of the organisms of choice for recombinant proteins because of its ability to grow at high density and availability of a vast catalog of cloning vectors and mutant host strains. Here, we describe the protocols for the expression of cold-adapted (hemo)globins in Escherichia coli.

Isolation of UV-Resistant Marine Bacteria by UV-C Assays.

Marine organisms have developed physiological and biochemical strategies to survive under the exposure of UV-B radiation. In particular, Antarctic marine bacteria, exposed to extremes of temperature, UV and ice, have adapted to cope with UV radiation by producing photoprotective molecules. Here, we describe (1) the sampling strategy to collect marine samples (surface water/ice and sediment samples) and (2) the selection strategy to isolate in these samples only UV-resistant marine bacteria.

Nitric Oxide Production and Regulation in the Teleost Cardiovascular System.

Nitric Oxide (NO) is a free radical with numerous critical signaling roles in vertebrate physiology. Similar to mammals, in the teleost system the generation of sufficient amounts of NO is critical for the physiological function of the cardiovascular system. At the same time, NO amounts are strictly controlled and kept within basal levels to protect cells from NO toxicity. Changes in oxygen tension highly influence NO bioavailability and can modulate the mechanisms involved in maintaining the NO balance. While NO production and signaling appears to have general similarities with mammalian systems, the wide range of environmental adaptations made by fish, particularly with regards to differing oxygen availabilities in aquatic habitats, creates a foundation for a variety of in vivo models characterized by different implications of NO production and signaling. In this review, we present the biology of NO in the teleost cardiovascular system and summarize the mechanisms of NO production and signaling with a special emphasis on the role of globin proteins in NO metabolism.

Ontogenetic shift and feeding habits of the European hake (Merluccius merluccius L., 1758) in Central and Southern Tyrrhenian Sea (Western Mediterranean Sea): A comparison between past and present data.

The present paper aims to investigate the ecological role of Merluccius merluccius, Linnaeus, 1758, in southern and central Tyrrhenian Sea (GSA 10, Resolution GFCM/33/2009/2 General Fisheries Commission for the Mediterranean), analyzing ontogenetic diet shifts, geographical variations on prey composition, and feeding habits. A total of 734 hake specimens ranging in size between 6 cm and 73 cm (Total Length, TL) were collected in 2018. In order to evaluate ontogenetic shifts in prey composition, samples were divided into five size classes and for each class the quantitative feeding indices have been calculated. The statistical analysis, based on index of relative importance percentage (%IRI), resulted in three trophic groups. The most abundant prey found in the immature hake specimens (size class I) were the Euphausiids, Stylocheiron longicorne and Mysidacea, while for samples with a total length over 10.5 cm were crustaceans and fish. Engraulis encrasicolus was the most abundant fish prey identified, followed by Boops boops and Myctophids. The high presence of Euphausiids, Mysids, Myctophidae, and Sternoptychidae in classes I, II, II, and IV (6-23 cm) showed the relevant role of mesopelagic fauna in hake diets, with an essential organic matter and energy flow from the mesopelagic to the epipelagic environment. Additionally, decapod crustaceans were found in the stomach contents of hakes belonging to class V (with size over 36 cm TL), which is notable considering that our study area includes an important decapod crustacean fishing area.

Bioactive Molecules from Extreme Environments II.

Marine organisms are known to produce a wide variety of natural products that are unique in terms of diversity, structural, and functional properties [...].

B cell activating factor (BAFF) from neutrophils and dendritic cells is required for protective B cell responses against Salmonella typhimurium infection.

Mice lacking B cells are more susceptible to S. typhimurium infection. How B cells contribute to protective immunity against Salmonella and what signals drive their activation are still unclear. Neutrophils (Nphs), monocytes (MOs), and dendritic cells (DCs) are involved in early immune responses to control the initial replication of S. typhimurium. These cells can produce B cell activating factor (BAFF) required for mature B cell survival and may help regulate B cell responses during Salmonella infection. Using BAFF reporter mice (BAFF-RFP+/-), we discovered that an i.p. infection with a virulent strain of S. typhimurium increased BAFF expression in splenic conventional DCs (cDC) and inflammatory Ly6Chi MOs/DCs four days post-infection. S. typhimurium infection induced the release of BAFF from Nphs, a decrease of BAFF-RFP expression and expansion of BAFF-RFP+ Nphs in the spleen and peritoneal cavity. After S. typhimurium infection, serum BAFF levels and immature and mature B cell subsets and plasma cells increased substantially. Conditional knockout (cKO) mice lacking BAFF in either Nphs or cDCs compared to control Bafffl/fl mice had reduced up-regulation of systemic BAFF levels and reduced expansion of mature and germinal center B cell subsets after infection. Importantly, the cKO mice lacking BAFF from either Nphs or cDCs had impaired induction of Salmonella-specific IgM Abs, and were more susceptible to S. typhimurium infection. Thus, Nphs and cDCs are major cellular sources of BAFF driving B cell responses, required for mounting optimal protective immunity against lethal Salmonella infection.

Bioactivity Screening of Antarctic Sponges Reveals Anticancer Activity and Potential Cell Death via Ferroptosis by Mycalols.

Sponges are known to produce a series of compounds with bioactivities useful for human health. This study was conducted on four sponges collected in the framework of the XXXIV Italian National Antarctic Research Program (PNRA) in November-December 2018, i.e., Mycale (Oxymycale) acerata, Haliclona (Rhizoniera) dancoi, Hemimycale topsenti, and Hemigellius pilosus. Sponge extracts were fractioned and tested against hepatocellular carcinoma (HepG2), lung carcinoma (A549), and melanoma cells (A2058), in order to screen for antiproliferative or cytotoxic activity. Two different chemical classes of compounds, belonging to mycalols and suberitenones, were identified in the active fractions. Mycalols were the most active compounds, and their mechanism of action was also investigated at the gene and protein levels in HepG2 cells. Of the differentially expressed genes, ULK1 and GALNT5 were the most down-regulated genes, while MAPK8 was one of the most up-regulated genes. These genes were previously associated with ferroptosis, a programmed cell death triggered by iron-dependent lipid peroxidation, confirmed at the protein level by the down-regulation of GPX4, a key regulator of ferroptosis, and the up-regulation of NCOA4, involved in iron homeostasis. These data suggest, for the first time, that mycalols act by triggering ferroptosis in HepG2 cells.

A Metataxonomic Approach Reveals Diversified Bacterial Communities in Antarctic Sponges.

Marine sponges commonly host a repertoire of bacterial-associated organisms, which significantly contribute to their health and survival by producing several anti-predatory molecules. Many of these compounds are produced by sponge-associated bacteria and represent an incredible source of novel bioactive metabolites with biotechnological relevance. Although most investigations are focused on tropical and temperate species, to date, few studies have described the composition of microbiota hosted by Antarctic sponges and the secondary metabolites that they produce. The investigation was conducted on four sponges collected from two different sites in the framework of the XXXIV Italian National Antarctic Research Program (PNRA) in November-December 2018. Collected species were characterized as Mycale (Oxymycale) acerata, Haliclona (Rhizoniera) dancoi, Hemigellius pilosus and Microxina sarai by morphological analysis of spicules and amplification of four molecular markers. Metataxonomic analysis of these four Antarctic sponges revealed a considerable abundance of Amplicon Sequence Variants (ASVs) belonging to the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia. In particular, M. (Oxymycale) acerata, displayed several genera of great interest, such as Endozoicomonas, Rubritalea, Ulvibacter, Fulvivirga and Colwellia. On the other hand, the sponges H. pilosus and H. (Rhizoniera) dancoi hosted bacteria belonging to the genera Pseudhongella, Roseobacter and Bdellovibrio, whereas M. sarai was the sole species showing some strains affiliated to the genus Polaribacter. Considering that most of the bacteria identified in the present study are known to produce valuable secondary metabolites, the four Antarctic sponges could be proposed as potential tools for the discovery of novel pharmacologically active compounds.

Decoding Brain Representations by Multimodal Learning of Neural Activity and Visual Features.

This work presents a novel method of exploring human brain-visual representations, with a view towards replicating these processes in machines. The core idea is to learn plausible computational and biological representations by correlating human neural activity and natural images. Thus, we first propose a model, EEG-ChannelNet, to learn a brain manifold for EEG classification. After verifying that visual information can be extracted from EEG data, we introduce a multimodal approach that uses deep image and EEG encoders, trained in a siamese configuration, for learning a joint manifold that maximizes a compatibility measure between visual features and brain representations. We then carry out image classification and saliency detection on the learned manifold. Performance analyses show that our approach satisfactorily decodes visual information from neural signals. This, in turn, can be used to effectively supervise the training of deep learning models, as demonstrated by the high performance of image classification and saliency detection on out-of-training classes. The obtained results show that the learned brain-visual features lead to improved performance and simultaneously bring deep models more in line with cognitive neuroscience work related to visual perception and attention.

Regulation of globin expression in Antarctic fish under thermal and hypoxic stress.

In the freezing waters of the Southern Ocean, Antarctic teleost fish, the Notothenioidei, have developed unique adaptations to cope with cold, including, at the extreme, the loss of hemoglobin in icefish. As a consequence, icefish are thought to be the most vulnerable of the Antarctic fish species to ongoing ocean warming. Some icefish also fail to express myoglobin but all appear to retain neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X. Despite the lack of the inducible heat shock response, Antarctic notothenioid fish are endowed with physiological plasticity to partially compensate for environmental changes, as shown by numerous physiological and genomic/transcriptomic studies over the last decade. However, the regulatory mechanisms that determine temperature/oxygen-induced changes in gene expression remain largely unexplored in these species. Proteins such as globins are susceptible to environmental changes in oxygen levels and temperature, thus playing important roles in mediating Antarctic fish adaptations. In this study, we sequenced the full-length transcripts of myoglobin, neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X from the Antarctic red-blooded notothenioid Trematomus bernacchii and the white-blooded icefish Chionodraco hamatus and evaluated transcripts levels after exposure to high temperature and low oxygen levels. Basal levels of globins are similar in the two species and both stressors affect the expression of Antarctic fish globins in brain, retina and gills. Temperature up-regulates globin expression more effectively in white-blooded than in red-blooded fish while hypoxia strongly up-regulates globins in red-blooded fish, particularly in the gills. These results suggest globins function as regulators of temperature and hypoxia tolerance. This study provides the first insights into globin transcriptional changes in Antarctic fish.

Bioactive Molecules from Extreme Environments.

Marine organisms inhabiting extreme habitats are a promising reservoir of bioactive compounds for drug discovery. Extreme environments, i.e., polar and hot regions, deep sea, hydrothermal vents, marine areas of high pressure or high salinity, experience conditions close to the limit of life. In these marine ecosystems, "hot spots" of biodiversity, organisms have adopted a huge variety of strategies to cope with such harsh conditions, such as the production of bioactive molecules potentially valuable for biotechnological applications and for pharmaceutical, nutraceutical and cosmeceutical sectors. Many enzymes isolated from extreme environments may be of great interest in the detergent, textile, paper and food industries. Marine natural products produced by organisms evolved under hostile conditions exhibit a wide structural diversity and biological activities. In fact, they exert antimicrobial, anticancer, antioxidant and anti-inflammatory activities. The aim of this Special Issue "Bioactive Molecules from Extreme Environments" was to provide the most recent findings on bioactive molecules as well as enzymes isolated from extreme environments, to be used in biotechnological discovery pipelines and pharmaceutical applications, in an effort to encourage further research in these extreme habitats.

Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions.

While the functions of the recently discovered cytoglobin, ubiquitously expressed in vertebrate tissues, remain uncertain, Antarctic fish provide unparalleled models to study novel protein traits that may arise from cold adaptation. We report here the spectral, ligand-binding and enzymatic properties (peroxynitrite isomerization, nitrite-reductase activity) of cytoglobin-1 from two Antarctic fish, Chaenocephalus aceratus and Dissostichus mawsoni, and present the crystal structure of D. mawsoni cytoglobin-1. The Antarctic cytoglobins-1 display high O2 affinity, scarcely compatible with an O2-supply role, a slow rate constant for nitrite-reductase activity, and do not catalyze peroxynitrite isomerization. Compared with mesophilic orthologues, the cold-adapted cytoglobins favor binding of exogenous ligands to the hexa-coordinated bis-histidyl species, a trait related to their higher rate constant for distal-His/heme-Fe dissociation relative to human cytoglobin. At the light of a remarkable 3D-structure conservation, the observed differences in ligand-binding kinetics may reflect Antarctic fish cytoglobin-1 specific features in the dynamics of the heme distal region and of protein matrix cavities, suggesting adaptation to functional requirements posed by the cold environment. Taken together, the biochemical and biophysical data presented suggest that in Antarctic fish, as in humans, cytoglobin-1 unlikely plays a role in O2 transport, rather it may be involved in processes such as NO detoxification.

Marine Terpenoids from Polar Latitudes and Their Potential Applications in Biotechnology.

Polar marine biota have adapted to thrive under one of the ocean's most inhospitable scenarios, where extremes of temperature, light photoperiod and ice disturbance, along with ecological interactions, have selected species with a unique suite of secondary metabolites. Organisms of Arctic and Antarctic oceans are prolific sources of natural products, exhibiting wide structural diversity and remarkable bioactivities for human applications. Chemical skeletons belonging to terpene families are the most commonly found compounds, whereas cytotoxic antimicrobial properties, the capacity to prevent infections, are the most widely reported activities from these environments. This review firstly summarizes the regulations on access and benefit sharing requirements for research in polar environments. Then it provides an overview of the natural product arsenal from Antarctic and Arctic marine organisms that displays promising uses for fighting human disease. Microbes, such as bacteria and fungi, and macroorganisms, such as sponges, macroalgae, ascidians, corals, bryozoans, echinoderms and mollusks, are the main focus of this review. The biological origin, the structure of terpenes and terpenoids, derivatives and their biotechnological potential are described. This survey aims to highlight the chemical diversity of marine polar life and the versatility of this group of biomolecules, in an effort to encourage further research in drug discovery.

Extending rnaSPAdes functionality for hybrid transcriptome assembly.

BACKGROUND: De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. RESULTS: In this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. CONCLUSION: To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.