The metabolic footprint of Vero E6 cells highlights the key metabolic routes associated with SARS-CoV-2 infection and response to drug combinations.

SARS-CoV-2 burdens healthcare systems worldwide, yet specific drug-based treatments are still unavailable. Understanding the effects of SARS-CoV-2 on host molecular pathways is critical for providing full descriptions and optimizing therapeutic targets. The present study used Nuclear Magnetic Resonance-based metabolic footprinting to characterize the secreted cellular metabolite levels (exometabolomes) of Vero E6 cells in response to SARS-CoV-2 infection and to two candidate drugs (Remdesivir, RDV, and Azithromycin, AZI), either alone or in combination. SARS-CoV-2 infection appears to force VE6 cells to have increased glucose concentrations from extra-cellular medium and altered energetic metabolism. RDV and AZI, either alone or in combination, can modify the glycolic-gluconeogenesis pathway in the host cell, thus impairing the mitochondrial oxidative damage caused by the SARS-CoV-2 in the primary phase. RDV treatment appears to be associated with a metabolic shift toward the TCA cycle. Our findings reveal a metabolic reprogramming produced by studied pharmacological treatments that protects host cells against virus-induced metabolic damage, with an emphasis on the glycolytic-gluconeogenetic pathway. These findings may help researchers better understand the relevant biological mechanisms involved in viral infection, as well as the creation of mechanistic hypotheses for such candidate drugs, thereby opening up new possibilities for SARS-CoV-2 pharmacological therapy.

The Formation of Carbon Dots from D-Glucose Studied by Infrared Spectroscopy.

Carbon dots (C-dots) obtained from D-glucose have attracted great interest because of their properties and as a model for understanding the synthesis process and the origin of photoluminescence in carbon-based nanostructures. Synthesising C-dots under hydrothermal conditions has become one of the most common methods for their preparation. Understanding the details of this process is quite difficult. To tackle this challenge, we have adopted a multi-technique approach in our present work. We have correlated different spectroscopic analyses, such as infrared, Raman, fluorescence, NMR, and UV-Vis, to connect the emissions with specific chemical groups. In particular, in situ infrared analysis as a function of temperature has allowed following the formation of C=C, C=O, and COOH species and the rise of specific emissions. Only weak emissions due to n-π* transitions are detected upon post-synthesis thermal annealing.

In Vitro Antiviral Activity of Hyperbranched Poly-L-Lysine Modified by L-Arginine against Different SARS-CoV-2 Variants.

The emergence of SARS-CoV-2 variants requires close monitoring to prevent the reoccurrence of a new pandemic in the near future. The Omicron variant, in particular, is one of the fastest-spreading viruses, showing a high ability to infect people and evade neutralization by antibodies elicited upon infection or vaccination. Therefore, the search for broad-spectrum antivirals that can inhibit the infectious capacity of SARS-CoV-2 is still the focus of intense research. In the present work, hyperbranched poly-L-lysine nanopolymers, which have shown an excellent ability to block the original strain of SARS-CoV-2 infection, were modified with L-arginine. A thermal reaction at 240 °C catalyzed by boric acid yielded Lys-Arg hyperbranched nanopolymers. The ability of these nanopolymers to inhibit viral replication were assessed for the original, Delta, and Omicron strains of SARS-CoV-2 together with their cytotoxicity. A reliable indication of the safety profile and effectiveness of the various polymeric compositions in inhibiting or suppressing viral infection was obtained by the evaluation of the therapeutic index in an in vitro prevention model. The hyperbranched L-arginine-modified nanopolymers exhibited a twelve-fold greater therapeutic index when tested with the original strain. The nanopolymers could also effectively limit the replication of the Omicron strain in a cell culture.

Quality Evaluation of Fresh Pasta Fortified with Sourdough Containing Wheat Germ and Wholemeal Semolina.

Pasta is a staple food in the Mediterranean diet, primarily manufactured with two essential ingredients, semolina and water; nowadays, it is often supplemented with functional ingredients. In this work, a sourdough obtained with wheat germ and wholemeal semolina was used, in order to improve sensorial and nutritional properties of fresh pasta, to prevent lipids oxidation, and to improve the shelf life. Three different formulations were prepared, a first one using semolina, a second one with raw wheat germ, wholemeal semolina, and semolina, and the last one with semolina and sourdough. The study highlighted the improved nutritional properties of pasta with sourdough (reduced phytic acid content, higher antioxidant activity and phenolic content). Proteins, ashes, dietary fibers, lipids, and tocols (vitamin E) increased in pasta with wheat germ and wholemeal semolina, and with sourdough. The amount of tocols decreased in pasta samples after cooking, except for the ß-tocopherol in sourdough pasta, the amount of which remained high, surprisingly. Lipase and lipoxygenase enzymes likely decreased as an effect of the pasteurization process. The NMR analysis showed that lipid oxidation was higher in semolina pasta than in pasta with wheat germ, most likely due to the protective effect of antioxidants deriving from wheat germ.

Shape-Persistent Dendrimers.

Dendrimers have a diverse and versatile morphology, frequently consisting of core, linking, and peripheral moieties. Dendrimers with flexible linkers, such as PAMAM, cannot retain the persistent shape of molecules, and this has been widely explored and reviewed previously; nevertheless, dendrimers with stiff linkers can preserve the persistent shape of the dendrimers, which has been reported considerably less. This review thus focuses on addressing shape-persistent dendrimers with rigid linking moieties discovered in recent years, i.e., from 2012 to 2023. Shape-persistent dendrimers with an interstitial gap between the dendritic frames in the solid state may or may not let the intramolecular void space be accessible for guest molecules, which largely depends on whether their peripheral groups are flexible or non-flexible. In this paper, eight articles on shape-persistent dendrimers with a flexible alkyl periphery, which may exhibit mesogenic phases upon thermal treatment, and eight articles on shape-persistent dendrimers with a non-flexible periphery, which may allow external ions, gases, or volatile organic compounds to access the interstitial gaps between dendritic frames, are reviewed.

Modulating the poly-L-lysine structure through the control of the protonation-deprotonation state of L-lysine.

Designing the architecture of L-lysine-based polymeric structures is a highly challenging task that requires careful control of the amino acid reactive groups. Conventional processes to obtain branched polylysine need several steps and the addition of specific catalysts. In the present work, to gain a better understanding and control of the formation of L-lysine-based polymers, we have investigated the correlation between the protonation state of L-lysine and the corresponding hydrothermally grown structures. The samples have been characterized by combining optical spectroscopies, such as UV-Vis, fluorescence, and synchrotron radiation circular dichroism with structural analysis by Nuclear Magnetic Resonance, Fourier Transform Infrared spectroscopy, and dynamic light scattering. We have observed that aqueous precursor solutions with alkaline pHs promote the formation of branched structures. In contrast, high pHs favour the reactivity of the ε-amino groups leading to linear structures, as shown by circular dichroism analyses. On the other hand, acidic conditions trigger the branching of the amino acid. Interestingly, the polymeric forms of L-lysine emit in the blue because the increasing number of intermolecular hydrogen bonds promote the intermolecular charge transfer responsible for the emission. Understanding the correlation between the L-lysine charged states and the polymeric structures that could form controlling the protonation-deprotonation states of the amino acid opens the route to a refined design of polypeptide systems based on L-lysine.

On the Compatibility of Fish Meal Replacements in Aquafeeds for Rainbow Trout. A Combined Metabolomic, Proteomic and Histological Study.

The sustainable development of modern aquaculture must rely on a significant reduction of the fish meal (FM) used in aquafeed formulations. However, FM substitution with alternative ingredients in diets for carnivorous fish species often showed reduced nutrient absorption, significantly perturbed metabolisms, and histological changes at both hepatic and intestinal levels. In the present study, rainbow trout (Oncorhynchus mykiss) were fed three different experimental aquafeeds. A control diet with higher FM content (27.3%) than two test formulations in which FM was substituted with two more sustainable and promising alternatives: insect meal (Hermetia illucens larvae = 10.1%, FM = 11.6%) and poultry by-products meal (PBM = 14.8%; FM = 11.7%). Combined metabolomics and proteomics analyses of fish liver, together with histological examination of liver and intestine demonstrated that a well-balanced formulation of nutrients in the three diets allowed high metabolic compatibility of either substitution, paving the way for a deeper understanding of the impact of novel raw materials for the fish feed industry. Results show that the main metabolic pathways of nutrient absorption and catabolism were essentially unaltered by alternative feed ingredients, and also histological alterations were negligible. It is demonstrated that the substitution of FM with sustainable alternatives does not have a negative impact on fish metabolism, as long as the nutritional requirements of rainbow trout are fulfilled.

Lipid metabolism of sea urchin Paracentrotus lividus in two contrasting natural habitats.

Sea urchins Paracentrotus lividus were harvested monthly from April 2015 to March 2016 from two sites in Sardinia (Italy). The two sites, a Posidonia oceanica meadow and a rocky bottom habitat, were naturally characterized by different food sources and availability, being mainly populated by the sea grass Posidonia oceanica and the brown algae Halopteris scoparia, respectively. Total lipids showed a minimum during winter in mature gonads, and a maximum in the summer (recovery stage). Fatty acid (FA) profiles of gut contents and gonads differed from those of the most available food sources. Levels of C18:3 (n-3) (ALA) discriminated samples from the two sites. Despite the very low amounts of C20:5 (n-3) (EPA) and C20:4 (n-6) (ARA) in P. oceanica, the main FA in gonads and gut contents were EPA and ARA in both sites. Increase in green algae intake prior to gametogenesis, especially C. cylindracea, likely affected EPA and ARA levels in gonads. The results show that P. lividus is able to concentrate lipids in gut contents and also to selectively store EPA, ARA and their precursors ALA and 18:2 (n-6) (LA). Moreover, bioconversion of ALA to EPA and of LA to ARA in P. lividus is suggested.

Metabolic response of yellow mealworm larvae to two alternative rearing substrates.

INTRODUCTION: Mass insect rearing is becoming increasingly pursued by food and feed industry due to its high sustainability and low environmental impact. Yellow mealworm larvae (Tenebrio molitor) are conventionally reared on wheat bran (WB), but alternative substrates, such as several by-products of the agri-food industry, have shown good prospects for insect rearing. OBJECTIVES: The objective of this study was to investigate on the metabolic and nutritional response of yellow mealworm larvae to dried brewer's spent grains (BSG) and WB used as rearing substrates. METHODS: Proximate, fibre and fatty acid compositions of durum WB and dried BSG were first characterized. Mealworm larvae were fed either WB (WB-L) or BSG (BSG-L) in a trial reproducing a scale rearing condition. Feed efficiency parameters together with proximate and FA composition were determined. Metabolic pathways affected by the dietary treatments were evaluated by means of a targeted metabolomics approach. Proton nuclear magnetic resonance (1H NMR) spectra were acquired on lipid and polar extracts of WB-L and BSG-L and then coupled to multivariate data analysis. Absolute quantitative 1H NMR data were carried out on selected metabolites. RESULTS: BSG-L exhibited better feed conversion ratio and efficiency in conversion of ingested food (P < 0.05) and almost half fat content (P < 0.001) than WB-L. BSG-L also showed higher ω-3 and ω-6 poliunsaturated fatty acids (P < 0.001) and lower content of monounsaturated fatty acids (P < 0.001) than WB-L. BSG-L mobilized body fat towards methylamine accumulation and led to enhanced trehalose catabolism. CONCLUSIONS: Our findings are useful to gain knowledge on the metabolic features that finally affect growth and body composition in reared yellow mealworm larvae.

Growing Trial of Gilthead Sea Bream (Sparus aurata) Juveniles Fed on Chironomid Meal as a Partial Substitution for Fish Meal.

Insect meal derived from chironomid larvae and collected from aquatic environments was included in the feed of gilthead sea bream juveniles (75 ± 1.1 g) in a growth trial of 90 days. Three feeds, which were namely one control (L1) and two experimental diets (L2, L3), were analyzed and formulated as isonitrogenous (45%) and isolipidic (13%). In L1, the protein source was mainly soybean meal (32%), followed by fish meal (20%), wheat meal (20%), gluten corn (17%), and hemoglobin (11%). In L2, the proportion of soybean meal was increased (33.5%), followed by gluten corn (21%), wheat meal (14%), and hemoglobin (11%), whereas the fish meal source was reduced (15%) due to the inclusion of chironomids (5%). In L3, the proportion of fish meal was further reduced (8%) and that of chironomid meal was increased to 10% of the protein source. The L2 and L3 groups showed similar growth performances with respect to the L1 group. The feed conversion rate was favorable in all the groups, ranging from 1.18 (L1) to 1.22 (L3). Survival rates varied from 93.62% (L3) to 94.31% (L1). Feed palatability showed similar results for all diets. Although the inclusion of chironomid meal was used in small quantities, our results suggest a significant advantage in replacing 50% of the fish meal with the chironomid meal for growing gilthead sea bream fishes.

The role of fatty acids and triglycerides in the gonads of Paracentrotus lividus from Sardinia: Growth, reproduction and cold acclimatization.

A detailed characterization of lipid extracts from gonads of P. lividus over a year has been performed combining GC and NMR measurements. For this purpose, sea urchins from two different Sardinian coastal areas were collected monthly. The results underlined a correlation between gonad fatty acids profiles and both water temperature and reproduction process. In particular, EPA and ARA appear to be the most altered fatty acids following seasonal changes. It is suggested that EPA could represent a biomarker of reproduction, reaching a content around 14% during gametogenesis, mainly due to an increase of the sn-1,3 position in TAGs. On the contrary, ARA seems to play a more important role in response to cold acclimatization, which is reflected in a modulation of ARA content in the sn-1,3 position in TAGs.

Molecular details on gilthead sea bream (Sparus aurata) sensitivity to low water temperatures from 1H NMR metabolomics.

Biometric and metabolic responses of gilthead sea bream to cold challenge are described following a growth trial divided into three water temperature steps, namely cooling, cold maintenance and recovery. Experimental data provide a useful description of fish response to thermal stress at both zootechnical and molecular level. Although no mortality has been observed, Nuclear Magnetic Resonance-based metabolomics confirms the marked sensitivity of this fish species to low water temperature, and explains some key molecular events associated to fish response to cold. Increase in hepatosomatic index is associated to liver fat accumulation, as a consequence of lipid mobilization from muscle and other extrahepatic tissues, and metabolic rearrangements linked to homeoviscous adaptation of cellular membranes are observed. Following primary responses to descending temperature from 18°C to 11°C, the energetic metabolism (insulin signaling, glycolysis) is first clearly affected; then, at constant low water temperature (11°C), the most perturbed metabolic pathways are related to methionine cycle in liver, while osmoregulatory function is exerted by TMAO in muscle. Water temperature recovery from 11°C to 18°C stimulates gluconeogenesis and glycogen synthesis activities at hepatic level, although the rate of a thermo-compensatory response seems to be slower than that of the cooling phase. The obtained results are intended to guide novel high-performance feed formulations for gilthead sea bream reared during winter.

Proteomic dataset of Paracentrotus lividus gonads of different sexes and at different maturation stages.

We report the proteomic dataset of gonads from wild Paracentrotus lividus related to the research article entitled "Proteomic changes occurring along gonad maturation in the edible sea urchin Paracentrotus lividus" [1]. Gonads of three individuals per sex in the recovery, pre-mature, mature, and spent stages were analyzed using a shotgun proteomics approach based on filter-aided sample preparation followed by tandem mass spectrometry, protein identification carried out using Sequest-HT as the search engine within the Proteome Discoverer informatics platform, and label-free differential analysis. The dataset has been deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD004200.

Proteomic changes occurring along gonad maturation in the edible sea urchin Paracentrotus lividus.

UNLABELLED: The reproductive stage of Paracentrotus lividus strongly influences product quality that, in turn, impacts significantly on the market price. Large, compact and sweet gonads are preferred, and sensory attributes are positively related to the ratio of nutritive phagocytes to gametes. Gonads at advanced maturation stages, although larger, have less desirable attributes, being more watery and bitter especially in females. Therefore, the best compromise among size, texture, and taste needs to be reached. In this study, wild P. lividus were collected along coastal Sardinia, and gonads in the recovery, pre-mature, mature, and spent stages were analyzed by gel-based and by shotgun proteomics. A detailed characterization of the proteome changes occurring in gonads of both sexes along maturation was achieved, and significant modifications were seen in numerous proteins involved in nutrient accumulation in nutritive phagocytes, as well as in gamete biology and maturation. Adding to an improved understanding of the P. lividus reproductive cycle in its natural environment, the results described in this work may form the basis for defining novel protein markers and procedures for an easier sexing and staging, and for monitoring sea urchin gonad maturation cycles in aquaculture plants. Mass spectrometry data are deposited in ProteomeXchange (PXD004200). SIGNIFICANCE: The sensory quality of P. lividus gonads is strongly influenced by the reproductive cycle, with significant changes in flavor, texture, and size. A better knowledge of the protein profiles, patterns, and markers associated with gonad sex and maturation stage can have useful implications for understanding and monitoring these changes. One of these is the ability to identify protein profiles specifically associated with a given stage and, in perspective, to identify maturation and sex markers. The comprehensive proteomic evaluation achieved in this work was made possible by the application of combined gel-based and shotgun approaches. As a result, this study generated the largest proteomic dataset available in the literature for P. lividus, as well as a general picture of protein abundance changes occurring along maturation.

Influence of seasonal and environmental patterns on the lipid content and fatty acid profiles in gonads of the edible sea urchin Paracentrotus lividus from Sardinia.

The influence of seasonal and environmental patterns on the lipid fraction of Paracentrotus lividus gonads was investigated. For this purpose, sea urchins were collected monthly over a year from two Sardinian coastal areas. Total lipids in gonads follow an annual cyclical trend, described by a sine wave curve, that it is more influenced by season than by growing area. The lowest lipid content in gonads corresponds to a high percentage of mature reproductive stages (i.e. winter season), independently of sampling area. A variation in total lipid content follows a change in photoperiod, while it is related to sea surface temperature. Multivariate analysis on fatty acid profiles of gonads, detected by gas chromatography, clusters the collected specimens mainly according to the sampling area, secondly according to the sites within the same sampling area and finally according to season.

Insights on the relaxation of liposomes encapsulating paramagnetic Ln-based complexes.

PURPOSE: To describe and quantify the different relaxation mechanisms operating in suspensions of liposomes that encapsulate paramagnetic lanthanide(III) complexes. THEORY AND METHODS: The transverse relaxation rate of lanthanide-loaded liposomes receives contribution from the exchange between intraliposomal and bulk water protons, and from magnetic susceptibility effects. Phospholipids vesicles encapsulating different Ln(III)-HPDO3A complexes (Ln = Eu, Gd, or Dy) were prepared using the conventional thin film rehydration method. Relaxation times (T1 , T2 , and T2*) were measured at 14 Tesla (T) and 25 °C. The effect of compartmentalization of the paramagnetic agent inside the liposomal cavity was evaluated by means of an IRON-modified MRI sequence. RESULTS: NMR measurements demonstrated that Curie spin relaxation is the dominant contribution (> 90%) to the observed transverse relaxation rate of paramagnetic liposomes. This was further confirmed by MRI that showed the ability of the liposome entrapped lanthanide complexes to generate IRON-MRI positive contrast in a size dependent manner. CONCLUSION: The Curie spin relaxation mechanism is by far the principal mechanism involved in the T2 shortening of the water protons in suspension of paramagnetic liposomes at 14T. The access to IRON contrast extends the potential of such nanosystems as MRI contrast agents.

Impact of three commercial feed formulations on farmed gilthead sea bream (Sparus aurata, L.) metabolism as inferred from liver and blood serum proteomics.

BACKGROUND: The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feeds, named A, B, and C, were subjected to lipid and protein characterization by gas chromatography (GC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. RESULTS: Feed B was higher in fish-derived lipids and proteins, while feeds C and A were higher in vegetable components, although the largest proportion of feed C proteins was represented by pig hemoglobin. According to biometric measurements, the feeds had significantly different impacts on fish growth, producing a higher average weight gain and a lower liver somatic index in feed B over feeds A and C, respectively. 2D DIGE/MS analysis of liver tissue and Ingenuity pathways analysis (IPA) highlighted differential changes in proteins involved in key metabolic pathways of liver, spanning carbohydrate, lipid, protein, and oxidative metabolism. In addition, serum proteomics revealed interesting changes in apolipoproteins, transferrin, warm temperature acclimation-related 65 kDa protein (Wap65), fibrinogen, F-type lectin, and alpha-1-antitrypsin. CONCLUSIONS: This study highlights the contribution of proteomics for understanding and improving the metabolic compatibility of feeds for marine aquaculture, and opens new perspectives for its monitoring with serological tests.

Biometric and metabolic profiles associated to different rearing conditions in offshore farmed gilthead sea bream (Sparus aurata L.).

Modern multivariate methods are applied to both biometric measurements and NMR metabolic profiling of fillet to discriminate farmed gilthead sea bream reared in different farming conditions. Two fish groups having the same average size, from the same farm, were caught in May and October. Biometric data demonstrate that condition factor is higher for the leaner fish, sampled in May, while liver somatic index is lower in fish sampled in October. Biometric features are related to metabolic changes that involve lipid storage from May to September, and their mobilization from muscle and liver during prespawning season (September, October). Structural phospholipids (phosphatidylcholine, phosphatidylethanolamine) and essential fatty acids (eicosapentaenoic and docosahexaenoic acids) characterize the lipid profile of the May catch, while triglycerides, monounsaturated and diunsaturated fatty acids, likely from absorption of vegetable oil components of feeds, suggest fish fattening in the warm season and discriminate fish caught in October. Among polar metabolites, taurine, glutamine, glycine, alanine, and creatine/phosphocreatine confirm their role as good biomarkers for the discrimination among fish produced in different farming conditions, especially involving feed digestion and metabolism, chronic stress, and alteration of energetic balance in cage-reared fish. Qualitative traits of farmed fish are therefore the result of a complex combination of environmental factors and farming practices, which should be analyzed to increase consumers' and farmers' awareness.

Multidisciplinary analytical investigation of phospholipids and triglycerides in offshore farmed gilthead sea bream (Sparus aurata) fed commercial diets.

In this work, a quantitative characterisation of lipid (both triglycerides and phospholipids) rearrangements in the muscle of offshore-raised gilthead sea bream was carried out as a function of fish growth between April and September. Relative percentages of lipid classes and fatty acids/acyls composition of the commercial feeds and fish dorsal muscles were assessed by means of an interdisciplinary analytical approach. A combination of preparative chemistry and experimental results from NMR spectroscopy, GC, 3D-TLC as well as proximate analysis permitted the observed growth parameters in key metabolic events to be linked with fish fattening and lipid turnover. While defined effects of feed composition on fatty acid profiles of fillets were ascertained, the relative increase of fatty acyls in triglycerides and phospholipids were also estimated enabling detailed evaluation of TAG:PL ratio in adult offshore-farmed gilthead sea bream. NMR was also used to quantify PUFA regiospecific distribution in TAG and PL.

Structural and Functional Characterization of a New Double Variant Haemoglobin (HbG-Philadelphia/Duarte α(2)ß(2)).

WE REPORT THE FIRST CASE OF COSEGREGATION OF TWO HAEMOGLOBINS (HBS): HbG-Philadelphia [α68(E17)Asn → Lys] and HbDuarte [ß62(E6)Ala → Pro]. The proband is a young patient heterozygous also for ß°-thalassaemia. We detected exclusively two haemoglobin variants: HbDuarte and HbG-Philadelphia/Duarte. Functional study of the new double variant HbG-Philadelphia/Duarte exhibited an increase in oxygen affinity, with a slight decrease of cooperativity and Bohr effect. This functional behaviour is attributed to ß62Ala → Pro instead of α68Asn → Lys substitution. Indeed, HbG-Philadelphia isolated in our laboratory from blood cells donor carrier for this variant is not affected by any functional modification, whereas purified Hb Duarte showed functional properties very similar to the double variant. NMR and MD simulation studies confirmed that the presence of Pro instead of Ala at the ß62 position produces displacement of the E helix and modifications of the tertiary structure. The substitution α68(E17)Asn → Lys does not cause significant structural and dynamical modifications of the protein. A possible structure-based rational of substitution effects is suggested.