A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling.

Cryptochromes are cardinal constituents of the circadian clock, which orchestrates daily physiological rhythms in living organisms. A growing body of evidence points to their participation in pathways that have not traditionally been associated with circadian clock regulation, implying that cryptochromes may be subject to modulation by multiple signaling mechanisms. In this study, we demonstrate that human CRY2 (hCRY2) forms a complex with the large, modular scaffolding protein known as Multi-PDZ Domain Protein 1 (MUPP1). This interaction is facilitated by the calcium-binding protein Calmodulin (CaM) in a calcium-dependent manner. Our findings suggest a novel cooperative mechanism for the regulation of mammalian cryptochromes, mediated by calcium ions (Ca2+ ) and CaM. We propose that this Ca2+ /CaM-mediated signaling pathway may be an evolutionarily conserved mechanism that has been maintained from Drosophila to mammals, most likely in relation to its potential role in the broader context of cryptochrome function and regulation. Further, the understanding of cryptochrome interactions with other proteins and signaling pathways could lead to a better definition of its role within the intricate network of molecular interactions that govern circadian rhythms.

Anion Exchange Membranes Based on Chemical Modification of Recycled PET Bottles.

This study presents an innovative and effective solution for recycling PET bottles as raw for producing anion exchange membranes (AEMs) for electrochemical applications. This approach reduces the demand for pristine materials, a key principle of the circular economy and sustainability. PET was subjected to chemical modification by introducing cationic functional groups followed by methylation and OH- exchange process. The amination synthesis was optimized based on reaction time. The results indicate that ion exchange capacity, water uptake, and swelling ratio properties mainly depend on the degree of cationic functionalization. The optimized AEM exhibits ionic conductivity of 5.3 × 10-2 S·cm-1 and alkaline stability of 432 h in 1 M KOH at 80 °C. The membrane properties before and after the alkaline treatment were investigated using Fourier-transform infrared spectroscopy, thermogravimetric analysis, and scanning electron microscopy analysis. Computational chemistry analysis was employed to gain further insights into the membrane degradation mechanisms and pathways under alkaline conditions. This research and its findings are a step toward using recycled materials in the field of AEM technology.

Impaired reproduction, energy reserves and dysbiosis: The overlooked consequences of heatwaves in a bivalve mollusc.

Extreme events like Marine Heatwaves (MHWs) are becoming more intense, severe, and frequent, threatening benthic communities, specifically bivalves. However, the consequences of non-lethal MHWs on animals are still poorly understood. Here, we exposed the Manila clam Ruditapes philippinarum to non-lethal MHW for 30 days and provided an integrative view of its effects. Our result indicated that albeit non-lethal, MHW reduced clam's energy reserves (by reducing their hepato-somatic index), triggered antioxidant defenses (particularly in males), impaired reproduction (via the production of smaller oocytes in females), triggered dysbiosis in the digestive gland microbiota and altered animals' behaviour (by impacting their burying capacity) and filtration rate. Such effects were seen also at RNA-seq (i.e. many down-regulated genes belonged to reproduction) and metabolome level. Interestingly, negative effects were more pronounced in males than in females. Our results show that MHWs influence animal physiology at multiple levels, likely impacting its fitness and its ecosystem services.

Activation of Vegetable Oils by Reaction with Maleic Anhydride as a Renewable Source in Chemical Processes: New Experimental and Computational NMR Evidence.

Vegetable oils are bio-based and sustainable starting materials that can be used to develop chemicals for industrial processes. In this study, the functionalization of three vegetable oils (grape, hemp, and linseed) with maleic anhydride was carried out either by conventional heating or microwave activation to obtain products that, after further reactions, can enhance the water dispersion of oils for industrial applications. To identify the most abundant derivatives formed, trans-3-octene, methyl oleate, and ethyl linoleate were reacted as reference systems. A detailed NMR study, supported by computational evidence, allowed for the identification of the species formed in the reaction of trans-3-octene with maleic anhydride. The signals in the 1H NMR spectra of the alkenyl succinic anhydride (ASA) moieties bound to the organic chains were clearly identified. The reactions achieved by conventional heating were carried out for 5 h at 200 °C, resulting in similar or lower amounts of ASA units/g of oil with respect to the reactions performed by microwave activation, which, however, induced a higher viscosity of the samples.

NMR Metabolite Profiles of the Bivalve Mollusc Mytilus galloprovincialis Before and After Immune Stimulation With Vibrio splendidus.

The hemolymph metabolome of Mytilus galloprovincialis injected with live Vibrio splendidus bacteria was analyzed by 1H-NMR spectrometry. Changes in spectral hemolymph profiles were already detected after mussel acclimation (3 days at 18 or 25 °C). A significant decrease of succinic acid was accompanied by an increase of most free amino acids, mytilitol, and, to a smaller degree, osmolytes. These metabolic changes are consistent with effective osmoregulation, and the restart of aerobic respiration after the functional anaerobiosis occurred during transport. The injection of Vibrio splendidus in mussels acclimated at 18°C caused a significant decrease of several amino acids, sugars, and unassigned chemical species, more pronounced at 24 than at 12 h postinjection. Correlation heatmaps indicated dynamic metabolic adjustments and the relevance of protein turnover in maintaining the homeostasis during the response to stressful stimuli. This study confirms NMR-based metabolomics as a feasible analytical approach complementary to other omics techniques in the investigation of the functional mussel responses to environmental challenges.

HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR.

Fragment-based lead discovery (FBLD) is one of the most efficient methods to develop new drugs. We present here a new computational protocol called High-Throughput Supervised Molecular Dynamics (HT-SuMD), which makes it possible to automatically screen up to thousands of fragments, representing therefore a new valuable resource to prioritise fragments in FBLD campaigns. The protocol was applied to Bcl-XL, an oncological protein target involved in the regulation of apoptosis through protein-protein interactions. Initially, HT-SuMD performances were validated against a robust NMR-based screening, using the same set of 100 fragments. These independent results showed a remarkable agreement between the two methods. Then, a virtual screening on a larger library of additional 300 fragments was carried out and the best hits were validated by NMR. Remarkably, all the in silico selected fragments were confirmed as Bcl-XL binders. This represents, to date, the largest computational fragments screening entirely based on MD.

Limited genotypic and geographic variability of 16-O-methylated diterpene content in Coffea arabica green beans.

The acknowledged marker of Robusta coffee, 16-O-methylcafestol (16-OMC), can be quantified by NMR as a mixture with 16-O-methylkahweol (16-OMK), which accounts for approximately 10% of the mixture. In the present study, we detected and quantified 16-O-methylated diterpenes (16-OMD) in 248 samples of green Coffea arabica beans by NMR. We did not observe any differences between genotypes introgressed by chromosomal fragments of Robusta and non-introgressed genotypes. Environmental effects suggesting a possible protective role of 16-OMD for adaptation, as well as genotypic effects that support a high heritability of this trait were observed. Altogether, our data confirmed the presence of 16-OMD in green Arabica at a level approximately 1.5% that of a typical Robusta, endorsing the validity of 16-OMD as a marker for the presence of Robusta.

A community-built calibration system: The case study of quantification of metabolites in grape juice by qNMR spectroscopy.

Nuclear Magnetic Resonance (NMR) is an analytical technique extensively used in almost every chemical laboratory for structural identification. This technique provides statistically equivalent signals in spite of using spectrometer with different hardware features and is successfully used for the traceability and quantification of analytes in food samples. Nevertheless, to date only a few internationally agreed guidelines have been reported on the use of NMR for quantitative analysis. The main goal of the present study is to provide a methodological pipeline to assess the reproducibility of NMR data produced for a given matrix by spectrometers from different manufacturers, with different magnetic field strengths, age and hardware configurations. The results have been analyzed through a sequence of chemometric tests to generate a community-built calibration system which was used to verify the performance of the spectrometers and the reproducibility of the predicted sample concentrations.

The lineage-specific, intrinsically disordered N-terminal extension of monothiol glutaredoxin 1 from trypanosomes contains a regulatory region.

Glutaredoxins (Grx) are small proteins conserved throughout all the kingdoms of life that are engaged in a wide variety of biological processes and share a common thioredoxin-fold. Among them, class II Grx are redox-inactive proteins involved in iron-sulfur (FeS) metabolism. They contain a single thiol group in their active site and use low molecular mass thiols such as glutathione as ligand for binding FeS-clusters. In this study, we investigated molecular aspects of 1CGrx1 from the pathogenic parasite Trypanosoma brucei brucei, a mitochondrial class II Grx that fulfills an indispensable role in vivo. Mitochondrial 1CGrx1 from trypanosomes differs from orthologues in several features including the presence of a parasite-specific N-terminal extension (NTE) whose role has yet to be elucidated. Previously we have solved the structure of a truncated form of 1CGrx1 containing only the conserved glutaredoxin domain but lacking the NTE. Our aim here is to investigate the effect of the NTE on the conformation of the protein. We therefore solved the NMR structure of the full-length protein, which reveals subtle but significant differences with the structure of the NTE-less form. By means of different experimental approaches, the NTE proved to be intrinsically disordered and not involved in the non-redox dependent protein dimerization, as previously suggested. Interestingly, the portion comprising residues 65-76 of the NTE modulates the conformational dynamics of the glutathione-binding pocket, which may play a role in iron-sulfur cluster assembly and delivery. Furthermore, we disclosed that the class II-strictly conserved loop that precedes the active site is critical for stabilizing the protein structure. So far, this represents the first communication of a Grx containing an intrinsically disordered region that defines a new protein subgroup within class II Grx.

Calmodulin Enhances Cryptochrome Binding to INAD in Drosophila Photoreceptors.

Light is the main environmental stimulus that synchronizes the endogenous timekeeping systems in most terrestrial organisms. Drosophila cryptochrome (dCRY) is a light-responsive flavoprotein that detects changes in light intensity and wavelength around dawn and dusk. We have previously shown that dCRY acts through Inactivation No Afterpotential D (INAD) in a light-dependent manner on the Signalplex, a multiprotein complex that includes visual-signaling molecules, suggesting a role for dCRY in fly vision. Here, we predict and demonstrate a novel Ca2+-dependent interaction between dCRY and calmodulin (CaM). Through yeast two hybrid, coimmunoprecipitation (Co-IP), nuclear magnetic resonance (NMR) and calorimetric analyses we were able to identify and characterize a CaM binding motif in the dCRY C-terminus. Similarly, we also detailed the CaM binding site of the scaffold protein INAD and demonstrated that CaM bridges dCRY and INAD to form a ternary complex in vivo. Our results suggest a process whereby a rapid dCRY light response stimulates an interaction with INAD, which can be further consolidated by a novel mechanism regulated by CaM.

Antiadhesive Activity and Metabolomics Analysis of Rat Urine after Cranberry (Vaccinium macrocarpon Aiton) Administration.

Cranberry (Vaccinium macrocarpon Aiton) is used to treat noncomplicated urinary tract infections (UTIs). A-type procyanidins (PAC-A) are considered the active constituents able to inhibit bacterial adhesion to the urinary epithelium. However, the role of PAC-A in UTIs is debated, because of their poor bioavailability, extensive metabolism, limited knowledge about urinary excretion, and contradictory clinical trials. The effects of 35-day cranberry supplementation (11 mg/kg PAC-A, 4 mg/kg PAC-B) were studied in healthy rats using a ultra performance liquid chromatography-mass spectrometry (UPLC-MS)-based metabolomics approach. Microbial PAC metabolites, such as valeric acid and valerolactone derivatives, were related to cranberry consumption. An increased urinary excretion of glucuronidated metabolites was also observed. In a further experiment, urine samples were collected at 2, 4, 8, and 24 h after cranberry intake and their antiadhesive properties were tested against uropathogenic Escherichia coli. The 8 h samples showed the highest activity. Changes in urinary composition were studied by ultra performance liquid chromatography-time-of-flight (UPLC-QTOF), observing the presence of PAC metabolites. The PAC-A2 levels were measured in all collected samples, and the highest amounts, on the order of ng/mL, were found in the samples collected after 4 h. Results indicate that the antiadhesive activity against uropathogenic bacteria observed after cranberry consumption is ascribable to PAC-A metabolites rather than to a direct PAC-A effect, as the measured PAC-A levels in urine was lower than those reported as active in the literature.

Studying the effects of natural extracts with metabolomics: A longitudinal study on the supplementation of healthy rats with Polygonum cuspidatum Sieb. et Zucc.

BACKGROUND: A longitudinal study was performed to evaluate the effects of Polygonum cuspidatum extract (standardized at 20% resveratrol) supplementation on healthy rats. The effects were explored by monitoring urinary metabolome changes using UPLC-HRMS and 1H NMR-based approaches. The aim of the study was to explore the effects of P. cuspidatum supplementation on a healthy animal model using metabolomics, in order to determine possible modes of action and obtain information on bioactivity. METHODS: Healthy Sprague-Dawley rats were orally supplemented with 100mg/kg of dried P. cuspidatum extract for 49days and 24-h urinary outputs were collected. Samples were analysed by untargeted UPLC-HRMS and 1H NMR approaches and the obtained data sets were modelled by an adaptation of post-transformation of PLS2 to longitudinal studies. Putative markers were discovered by a stability selection procedure and specific oxidative stress markers were monitored by a targeted HPLC-MS/MS analysis to assess the in vivo antioxidant activity of P. cuspidatum extract. RESULTS: UPLC-HRMS and 1H NMR platforms showed two different but complementary patterns of metabolites describing the changes ascribable to P. cuspidatum supplementation and using both approaches, a comprehensive resveratrol metabolism and urinary excretion could be observed. Markers of P. cuspidatum supplementation effects identified by UPLC-HRMS were mainly related to its antioxidant activity and to a possible "adaptogenic" activity. Urinary changes observed by 1H NMR were mainly related to energy metabolism. UPLC-HRMS and 1H NMR metabolomics approaches allowed the effects of a prolonged supplementation with P. cuspidatum on healthy rats to be observed. The statistical models built from both data sets showed metabolic changes in urines related to rat aging.

A molecular dynamics strategy for CSαß peptides disulfide-assisted model refinement.

Many cysteine-stabilized antimicrobial peptides from a variety of living organisms could be good candidates for the development of anti-infective agents. In the absence of experimentally obtained structural data, peptide modeling is an essential tool for understanding structure-activity relationships and for optimizing the bioactive moieties. Focusing on cysteine-rich peptide structures, we reproduced the case of structure predictions in the so-called midnight zone. We developed our protocol on a training set derived by clustering the available cysteine-stabilized αß (CSαß) structures in nine different representative families and tested it on peptides randomly selected from each family. Starting from draft models, we tested a structure-based disulfide predictor and we used cysteine distances as constraints during molecular dynamics. Finally, we proposed an analysis for final structure selection. Accordingly, we obtained a mean root mean square deviation improvement of 21% for the test set. Our findings demonstrate that it is possible to predict the network of disulfide bridges in cysteine-stabilized peptides and to use this result to improve the accuracy of structural predictions. Finally, we applied the methods to predict the structure of royalisin, a cysteine-rich peptide with unknown structure.

Objective Definition of Monofloral and Polyfloral Honeys Based on NMR Metabolomic Profiling.

In this paper, a remarkably precise, simple, and objective definition of monofloral and polyfloral honey based on NMR metabolomics is proposed. The spectra of organic extracts of 983 samples of 16 botanical origins were used to derive one-versus-all OPLS-DA classification models. The predictive components of the statistical models reveal not only the principal but also the secondary floral origins present in a sample of honey, a novel feature with respect to the methods present in the literature that are able to confirm the authenticity of monofloral honeys but not to characterize a mixture of honey types. This result descends from the peculiar features of the chloroform spectra that show diagnostic resonances for almost each botanical origin, making these NMR spectra suitable fingerprints. The reliability of the method was tested with an additional 120 samples, and the class assignments were compared with those obtained by traditional analysis. The two approaches are in excellent agreement in identifying the floral species present in honeys and in the botanical classification. Therefore, this NMR method may prove to be a valid solution to the huge limitations of traditional classification, which is very demanding and complex.

1H, 13C and 15N resonance assignment of the cytosolic dithiol glutaredoxin 1 from the pathogen Trypanosoma brucei.

Trypanosomatids are parasites responsible for several tropical and subtropical diseases, such as Chaga's disease, sleeping sickness and Leishmaniasis. In contrast to the mammalian host, the thiol-redox metabolism of these pathogens depends on trypanothione [bis-glutathionylspermidine, T(SH)2] instead of glutathione (GSH) providing a set of lineage-specific proteins as drug target candidates. Glutaredoxins (Grx) are ubiquitous small thiol-disulfide oxidoreductases that belong to the thioredoxin-fold family. They play a central role in redox homeostasis and iron sulfur-cluster biogenesis. Each species, including trypanosomes, possesses its own set of isoforms distributed in different subcellular compartments. The genome of trypanosomatids encodes for two class I (dithiolic) Grxs named 2-C-Grx1 and 2-C-Grx2. Both proteins were shown to efficiently reduce different disulfides at the expenses of T(SH)2 using a mechanism that involves the two cysteines in the active site. Moreover, the cytosolic Trypanosoma brucei 2-C-Grx1 but not the mitochondrial 2-C-Grx2 was able to coordinate an iron-sulfur cluster with T(SH)2 or GSH as ligand. As a first step to unravel the structural basis for the specificity observed in the trypanosomal glutaredoxins, we present here the NMR resonance assignment of 2-C-Grx1 from the parasite T. brucei brucei.

New findings on the in vivo antioxidant activity of Curcuma longa extract by an integrated (1)H NMR and HPLC-MS metabolomic approach.

Curcuminoids possess powerful antioxidant activity as demonstrated in many chemical in vitro tests and in several in vivo trials. Nevertheless, the mechanism of this activity is not completely elucidated and studies on the in vivo antioxidant effects are still needed. Metabolomics may be used as an attractive approach for such studies and in this paper, we describe the effects of oral administration of a Curcuma longa L. extract (150 mg/kg of total curcuminoids) to 12 healthy rats with particular attention to urinary markers of oxidative stress. The experiment was carried out over 33 days and changes in the 24-h urine samples metabolome were evaluated by (1)H NMR and HPLC-MS. Both techniques produced similar representations for the collected samples confirming our previous study. Modifications of the urinary metabolome lead to the observation of different variables proving the complementarity of (1)H NMR and HPLC-MS for metabolomic purposes. The urinary levels of allantoin, m-tyrosine, 8-hydroxy-2'-deoxyguanosine, and nitrotyrosine were decreased in the treated group thus supporting an in vivo antioxidant effect of the oral administration of Curcuma extract to healthy rats. On the other hand, urinary TMAO levels were higher in the treated compared to the control group suggesting a role of curcumin supplementation on microbiota or on TMAO urinary excretion. Furthermore, the urinary levels of the sulphur containing compounds taurine and cystine were also changed suggesting a role for such constituents in the biochemical pathways involved in Curcuma extract bioactivity and indicating the need for further investigation on the complex role of antioxidant curcumin effects.

Structural and Antimicrobial Features of Peptides Related to Myticin C, a Special Defense Molecule from the Mediterranean Mussel Mytilus galloprovincialis.

Mussels (Mytilus spp.) have a large repertoire of cysteine-stabilized α,ß peptides, and myticin C (MytC) was identified in some hundreds of transcript variants after in vivo immunostimulation. Using a sequence expressed in Italian mussels, we computed the MytC structure and synthesized the mature MytC and related peptide fragments (some of them also prepared in oxidized form) to accurately assess their antibacterial and antifungal activity. Only when tested at pH 5 was the reduced MytC as well as reduced and oxidized fragments including structural ß-elements able to inhibit Gram-positive and -negative bacteria (MIC ranges of 4-32 and 8-32 µM, respectively). Such fragments caused selective Escherichia coli killing (MBC of 8-32 µM) but scarcely inhibited two fungal strains. In detail, the antimicrobial ß-hairpin MytC[19-40]SOX caused membrane-disrupting effects in E. coli despite its partially ordered conformation in membrane-mimetic environments. In perspective, MytC-derived peptides could be employed to protect acidic mucosal tissues, in cosmetic and food products, and, possibly, as adjuvants in aquaculture.

Quantification of caffeine in human saliva by Nuclear Magnetic Resonance as an alternative method for cytochrome CYP1A2 phenotyping.

The first step in caffeine metabolism is mediated for over 95% by the CYP1A2 isoform of cytochrome P450. Therefore, CYP1A2 activity is most conveniently measured through the determination of caffeine clearance. The HPLC quantification of caffeine is fully validated and is the most widely used method. It can be performed on saliva, which is gaining importance as a diagnostic biofluid and permits easy and low invasive sampling. Here, we present a quantitative (1)H nuclear magnetic resonance (NMR) method to determine caffeine in human saliva. The procedure is simple because it involves only an ultra-filtration step and a direct extraction in a deuterated solvent, yielding a matrix that is then analyzed. The reliability of this NMR method was demonstrated in terms of linearity, accuracy, recovery, and limits of detection (LoD). Good precision (relative standard deviation, RSD <4%), a recovery of >95% and LoD of 6.8·10(-7) mol L(-1) were obtained. The method was applied to samples collected from different volunteers over 24h following a single oral dose of about 100mg of caffeine administered with either coffee beverage or a capsule.

Preliminary Characterization of Monofloral Coffea spp. Honey: Correlation between Potential Biomarkers and Pollen Content.

To determine the botanical origin of Coffea honey, a new method using proton nuclear magnetic resonance ((1)H NMR) is proposed. Integration of the aromatic region of the NMR spectrum of Coffea honey diluted in deuterated water allowed us to simultaneously quantify caffeine, theobromine, and trigonelline, as well as other compounds. The amounts of the three markers listed are significantly higher than those previously reported for Citrus spp. honey: caffeine ranged from 15 to 98 mg/kg, theobromine from 25 to 160 mg/kg, and trigonelline from 23 to 86 mg/kg. The concurrent presence of these three substances is proposed as an indicator of the botanical origin of Coffea honey. Excellent correlation was found between these markers and the relative amounts of Coffea pollen measured in the same samples.