Dimeric phenanthrenoids: possible biogenetic pathway and missing compounds.

Secondary metabolites extracted from plants have historically been critical for drug discovery, but their isolation involves expensive and complicated procedures in terms of time and labor resources. Thus, the biogenetic pathway offers the possibility of identifying specific compounds that have not yet been isolated and predicting their isolation from specific natural sources. In plants, biphenanthrenes represent a relatively small group of aromatic secondary metabolites that are considered as important taxonomic markers with promising biological activities. To date, 38 mixed phenanthrenoid dimers have been identified, the biosynthesis of which involves the radical coupling of the two subunits, namely, a phenanthrene and a dihydrophenanthrene. For each of the compounds, it is possible to identify the single phenanthrenic and dihydrophenanthrenic units constituting the considered dimer. Based on the biogenetic pathway, it is possible to identify 19 phenanthrenes and 17 dihydrophenanthrenes, and to distinguish those already known from those not yet isolated. By comparing the results of the possible biosynthetic pathway for each compound with the data in the literature, it is possible to identify three known phenanthrenes and seven known dihydrophenanthrenes, as well as eleven new phenanthrenes and five new dihydrophenanthrenes, and to identify from which plant it is possible to isolate them. This could direct the work of researchers seeking to identify known or new molecules useful for their possible biological properties, and ultimately, to confirm the veracity of the proposed and generally accepted biosynthetic pathway.

Temperature sensitivity and decomposition rate of 101 leaf litter types from Mediterranean ecosystems.

Litter decomposition is a fundamental process, and the number of published studies has steadily increased in recent decades. However, few experiments have systematically compared a large number of litter types and evaluated their temperature sensitivity. We conducted a two-year experiment on the decomposition of litter bags containing 101 leaf litter sampled in Mediterranean ecosystems and incubated under laboratory conditions at 4 °C, 14 °C, and 24 °C. Litter was chemically characterized and analysed for carbon (C), nitrogen (N), cellulose and lignin concentration, C/N, and lignin/N ratios, which serve as predictors of decomposition rate. The sensitivity of litter decay rate to temperature was evaluated using Q10. Leaf litter chemistry varied widely in nitrogen content (range 0.52-6.80 %), lignin content (range 1.53-49.31 %), C/N ratio (range 5.21-77.78), and lignin/N ratio (range 0.34-34.90). Litter decomposition rate was negatively related to initial lignin concentration, lignin/N ratio, and C/N ratio, but only in the early stage. In the late stages of decomposition, litter decay rate was negatively correlated with initial N concentration but positively correlated with C/N and lignin/N ratios. Temperature sensitivity was negatively correlated with N concentration and positively correlated with lignin and lignin/N ratio. It is noteworthy that, contrary to expectations, temperature sensitivity exhibited a hump-shaped relationship with decay rate. N, C/N, and lignin/N ratios should be used with caution because their predictive power is reversed with respect to decomposition rate during the decomposition process. In addition, the new finding that temperature sensitivity has a hump-shaped relationship with decomposition rate deserves further confirmation and could be considered in ecosystem-level organic C modeling.

A pan-influenza antibody inhibiting neuraminidase via receptor mimicry.

Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift1 and suboptimal immune responses2. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.

Anthropic impact on soil heavy metal contamination in riparian ecosystems of northern Algeria.

The aim of this research was to highlight the impact of urbanization and agriculture on soil quality, mainly by focusing on heavy metal accumulation (Cd, Cu, Fe, Mn, Ni, Pb and Zn) in the fragile riparian ecosystems of the Medjerda river (Souk-Ahras, Algeria). This study was performed in three cultivated soils (0-10, 10-20, 20-60 cm depth) along an increasing gradient of anthropogenic pressure in non-urban (NU), peri-urban (PU) and urban areas (U). Geo-accumulation index (Igeo), Enrichment factor (EF), Pollution load index (PLI) and Potential ecological risk index (RI) were calculated, as well as the potential non-carcinogenic risk for humans (HI). Additionally, to corroborate the role of Bufo spinosus D. as biosentinel, a skin biopsy was performed to quantify the concentration of heavy metals in both terrestrial and aquatic ecosystems. The results showed that when compared to NU, U and PU areas were richer in heavy metals. In particular, Igeo-Cd displayed strongly contaminated soil in U (>3), EF showed high enrichment of heavy metals (>2) for all the soils except for Ni, PLI presented no contamination for all (<1) while RI was significantly higher in U (>300), denoting a strong impact of heavy metals on soil quality. However, HI was below 1 for all the studied areas, although the highest values were related to U and PU. The skin biopsy showed the highest values for Cu, Fe and Pb in PU (0.328, 0.713 and 0.524 mg kg-1, respectively) similarly to trends observed in the soil of that area. This study shed light on the rising pollution of heavy metals due to urbanization and agricultural input in these fragile ecosystems where Bufo spinosus D. plays the role of potential bio-indicator for environmental pollution.

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development.

Chemical, Functional, and Technological Features of Grains, Brans, and Semolina from Purple and Red Durum Wheat Landraces.

A main reason of the increasing interest in cereal landraces is their potential to offer more diversified and functional staple food. For instance, landraces are an underexploited resource of pigmented varieties, appreciated for the high accumulation of phytochemicals with known health benefits. This study characterized the chemical, functional, and technological features of the bran, semolina, and grains of two durum wheat (Triticum turgidum L. subsp. durum, Desf.) landraces, named 'Purple' and 'Red' for their grain color, collected in Ethiopia and grown and sold in southern Italy as a niche product. Specifically, we analyzed the protein content, dry gluten, ash, total polyphenols, anthocyanins, proanthocyanidins, and specific phenolic acids. We also evaluated the antioxidant activity using DPPH- and ABTS-based methods. The two landraces had positive nutritional features, such as a high protein content, a rich and composite range of secondary metabolites (which include specific phenolic acids and anthocyanins), and antioxidant activities in all the fractions analyzed. The germplasm under investigation therefore has a well-justified potential to yield functional products and to diversify durum wheat-based foods.

Ion-bridges and lipids drive aggregation of same-charge nanoparticles on lipid membranes.

The control of the aggregation of biomedical nanoparticles (NP) in physiological conditions is crucial as clustering may change completely the way they interact with the biological environment. Here we show that Au nanoparticles, functionalized by an anionic, amphiphilic shell, spontaneously aggregate in fluid zwitterionic lipid bilayers. We use molecular dynamics and enhanced sampling techniques to disentangle the short-range and long-range driving forces of aggregation. At short inter-particle distances, ion-mediated, charge-charge interactions (ion bridging) stabilize the formation of large NP aggregates, as confirmed by cryo-electron microscopy. Lipid depletion and membrane curvature are the main membrane deformations driving long-range NP-NP attraction. Ion bridging, lipid depletion, and membrane curvature stem from the configurational flexibility of the nanoparticle shell. Our simulations show, more in general, that the aggregation of same-charge membrane inclusions can be expected as a result of intrinsically nanoscale effects taking place at the NP-NP and NP-bilayer soft interfaces.

Impact of prescribed burning, mowing and abandonment on a Mediterranean grassland: A 5-year multi-kingdom comparison.

Mediterranean grasslands are semi-natural, fire-prone, species-rich ecosystems that have been maintained for centuries through a combination of fire, grazing, and mowing. Over the past half century, however, grasslands have faced numerous threats, including the abandonment of traditional agro-pastoral practices. Our hypothesis was that mowing and prescribed burning are management practices potentially effective in counteracting the reduction of plant diversity triggered by land abandonment. However, the long-term effects of such management practices on plant communities and soil microbiota in Mediterranean grassland remain poorly studied. Here, we conducted a 5-year field experiment comparing prescribed fire, vegetation mowing, and abandonment in a fire-prone Mediterranean grassland in southern Italy in order to evaluate the capability of such management strategies to counteract the detrimental impacts of land abandonment on plant diversity and the associated increase of wildfire. We combined vegetation analysis and soil chemical characterization and several microbiota analyses, including microbial biomass and respiration, arthropod community, and high-throughput sequencing of bacterial and eukaryotic rRNA gene markers. Burning and mowing significantly increased plant species richness and diversity compared to abandonment plots, reducing the abundance of perennial tall grasses in favour of short-lived species. Standing litter followed the same trend, being 3.8-fold greater and largely composed of grass remains in the abandoned compared to burnt and mowed plots. In the soil, prescribed burning caused significant increase in pH, a reduction in organic carbon, total N, and cation exchange capacity. Diversity and taxonomic composition of bacterial and fungal microbiota was affected by burning and mowing treatments. Abandonment caused shifts of microbiota towards a fungal-dominated system, composed of late successional fungi of the Basidiomycota. Fast-growing and putative fungal pathogens were more abundant under burnt and mowed treatments. Soil arthropods were influenced by vegetation and microbiota changes, being strongly reduced in mowed plots. Our study demonstrated that grassland abandonment promotes the spread of tall grasses, reducing plant diversity and increasing the risk of wildfire, while prescribed burning and mowing are effective in counteracting such negative effects.

Molecular communications in complex systems of dynamic supramolecular polymers.

Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which intrinsic dynamics is hard to elucidate. Here we report coarse-grained molecular simulations that allow studying supramolecular polymers at the thermodynamic equilibrium, explicitly showing the complex nature of these systems, which are composed of exquisitely dynamic molecular entities. Detailed studies of molecular exchange provide insights into key factors controlling how assemblies communicate with each other, defining the equilibrium dynamics of the system. Using minimalistic and finer chemically relevant molecular models, we observe that a rich concerted complexity is intrinsic in such self-assembling systems. This offers a new dynamic and probabilistic (rather than structural) picture of supramolecular polymer systems, where the travelling molecular species continuously shape the assemblies that statistically emerge at the equilibrium.

Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.

The SARS-CoV-2 Omicron BA.1 variant emerged in 20211 and has multiple mutations in its spike protein2. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways3 demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.

Soil Biological Responses under Different Vegetation Types in Mediterranean Area.

The knowledge of the effects of fire on soil properties is of particular concern in Mediterranean areas, where the effects of vegetation type are still scarce also. This research aimed: to assess the properties of burnt soils under different vegetation types; to highlight the soil abiotic properties driving the soil microbial biomass and activity under each vegetation type; to compare the biological response in unburnt and burnt soils under the same vegetation type, and between unburnt and burnt soils under different vegetation types. The soils were collected at a Mediterranean area where a large wildfire caused a 50% loss of the previous vegetation types (holm oak: HO, pine: P, black locust: BL, and herbs: H), and were characterized by abiotic (pH, water, and organic matter contents; N concentrations; and C/N ratios) and biotic (microbial and fungal biomasses, microbial respiration, soil metabolic quotient, and hydrolase and dehydrogenase activities) properties. The biological response was evaluated by the Integrative Biological Responses (IBR) index. Before the fire, organic matter and N contents were significantly higher in P than H soils. After the fire, significant increases of pH, organic matter, C/N ratio, microbial biomass and respiration, and hydrolase and dehydrogenase activities were observed in all the soils, especially under HO. In conclusion, the post-fire soil conditions were less favorable for microorganisms, as the IBR index decreased when compared to the pre-fire conditions.

Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.

Understanding broadly neutralizing sarbecovirus antibody responses is key to developing countermeasures against SARS-CoV-2 variants and future zoonotic sarbecoviruses. We describe the isolation and characterization of a human monoclonal antibody, designated S2K146, that broadly neutralizes viruses belonging to SARS-CoV- and SARS-CoV-2-related sarbecovirus clades which use ACE2 as an entry receptor. Structural and functional studies show that most of the virus residues that directly bind S2K146 are also involved in binding to ACE2. This allows the antibody to potently inhibit receptor attachment. S2K146 protects against SARS-CoV-2 Beta challenge in hamsters and viral passaging experiments reveal a high barrier for emergence of escape mutants, making it a good candidate for clinical development. The conserved ACE2-binding residues present a site of vulnerability that might be leveraged for developing vaccines eliciting broad sarbecovirus immunity.

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift.

The recently emerged SARS-CoV-2 Omicron variant encodes 37 amino acid substitutions in the spike protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody-based therapeutics. Here we show that the Omicron RBD binds to human ACE2 with enhanced affinity, relative to the Wuhan-Hu-1 RBD, and binds to mouse ACE2. Marked reductions in neutralizing activity were observed against Omicron compared to the ancestral pseudovirus in plasma from convalescent individuals and from individuals who had been vaccinated against SARS-CoV-2, but this loss was less pronounced after a third dose of vaccine. Most monoclonal antibodies that are directed against the receptor-binding motif lost in vitro neutralizing activity against Omicron, with only 3 out of 29 monoclonal antibodies retaining unaltered potency, including the ACE2-mimicking S2K146 antibody1. Furthermore, a fraction of broadly neutralizing sarbecovirus monoclonal antibodies neutralized Omicron through recognition of antigenic sites outside the receptor-binding motif, including sotrovimab2, S2X2593 and S2H974. The magnitude of Omicron-mediated immune evasion marks a major antigenic shift in SARS-CoV-2. Broadly neutralizing monoclonal antibodies that recognize RBD epitopes that are conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.

Phenanthrene Dimers: Promising Source of Biologically Active Molecules.

To date, just over a hundred phenanthrenoid dimers have been isolated. Of these, forty-two are completely phenanthrenic in nature. They are isolated from fourteen genera of different plants belonging to only five families, of which Orchidaceae is the most abundant source. Other nine completely acetylated and five methylated dimers were also defined, which were effective in establishing the position of the free hydroxyls of the corresponding natural products, from which they were obtained by semi-synthesis. Structurally, they could be useful chemotaxonomic markers considering that some substituents are typical of a single-family, such as the vinyl group for Juncaceae. From a biogenetic point of view, it is thought that these compounds derive from the radical coupling of the corresponding phenanthrenes or by dehydrogenation of the dihydrophenanthrenoid analogs. Phenanthrenes or dihydroderivatives possess different biological activities, e.g., antiproliferative, antimicrobial, antiinflammatory, antioxidant, spasmolytic, anxiolytic, and antialgal effects. The aim of this review is to summarize the occurrence of phenanthrene dimers in the different natural sources and give a comprehensive overview of their structural characteristics and biological activities.

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift.

The recently emerged SARS-CoV-2 Omicron variant harbors 37 amino acid substitutions in the spike (S) protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics. Here, we show that the Omicron RBD binds to human ACE2 with enhanced affinity relative to the Wuhan-Hu-1 RBD and acquires binding to mouse ACE2. Severe reductions of plasma neutralizing activity were observed against Omicron compared to the ancestral pseudovirus for vaccinated and convalescent individuals. Most (26 out of 29) receptor-binding motif (RBM)-directed monoclonal antibodies (mAbs) lost in vitro neutralizing activity against Omicron, with only three mAbs, including the ACE2-mimicking S2K146 mAb 1 , retaining unaltered potency. Furthermore, a fraction of broadly neutralizing sarbecovirus mAbs recognizing antigenic sites outside the RBM, including sotrovimab 2 , S2X259 3 and S2H97 4 , neutralized Omicron. The magnitude of Omicron-mediated immune evasion and the acquisition of binding to mouse ACE2 mark a major SARS-CoV-2 mutational shift. Broadly neutralizing sarbecovirus mAbs recognizing epitopes conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.

Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of infections and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing their immune evasion. Mutations in the B.1.617.1 (Kappa) and Delta spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including remodeling of the Delta amino-terminal domain. The angiotensin-converting enzyme 2 binding affinities of the Kappa and Delta receptor binding domains are comparable to the Wuhan-Hu-1 isolate, whereas B.1.617.2+ (Delta+) exhibits markedly reduced affinity.

Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.

Understanding broadly neutralizing sarbecovirus antibody responses is key to developing countermeasures effective against SARS-CoV-2 variants and future spillovers of other sarbecoviruses. Here we describe the isolation and characterization of a human monoclonal antibody, designated S2K146, broadly neutralizing viruses belonging to all three sarbecovirus clades known to utilize ACE2 as entry receptor and protecting therapeutically against SARS-CoV-2 beta challenge in hamsters. Structural and functional studies show that most of the S2K146 epitope residues are shared with the ACE2 binding site and that the antibody inhibits receptor attachment competitively. Viral passaging experiments underscore an unusually high barrier for emergence of escape mutants making it an ideal candidate for clinical development. These findings unveil a key site of vulnerability for the development of a next generation of vaccines eliciting broad sarbecovirus immunity.