Biosensor surface functionalization by a simple photochemical immobilization of antibodies: experimental characterization by mass spectrometry and surface enhanced Raman spectroscopy

Surface functionalization is a key step in biosensing since it is the basis of an effective analyte recognition. Among all the bioreceptors, antibodies (Abs) play a key role thanks to their superior specificity, although the available immobilization strategies suffer from several drawbacks. When gold is the interacting surface, the recently introduced Photochemical Immobilization Technique (PIT) has been shown to be a quick, easy-to-use and very effective method to tether Abs oriented upright by means of thiols produced via tryptophan mediated disulphide bridge reduction. Although the molecular mechanism of this process is quite well identified, the detailed morphology of the immobilized antibodies is still elusive due to inherent difficulties related to the microscopy imaging of Abs. The combination of Mass Spectrometry, Surface-Enhanced Raman Spectroscopy and Ellman's assay demonstrates that Abs irradiated under the conditions in which PIT is realized show only two effective disulphide bridges available for binding. They are located in the constant region of the immunoglobulin light chain so that the most likely position Ab assumes is side-on, i.e. with one Fab (i.e. the antigen binding portion of the antibody) exposed to the solution. This is not a limitation of the recognition efficiency in view of the intrinsic flexibility of the Ab structure, which makes the free Fab able to sway in the solution, a feature of great importance in many biosensing applications.

Variation in prostaglandin metabolism during growth of the diatom Thalassiosira rotula

Prostaglandins (PGs) are hormone-like mediators in many physiological and pathological processes that are present in all vertebrates, in some terrestrial and aquatic invertebrates, and have also been identified in some macroalgae. They have recently been reported also in marine microalgae but their role as chemical mediators is largely unknown. Here we studied the expression pattern of the PG biosynthetic pathway during different growth phases of the centric diatom Thalassiosira rotula and assessed the release of PGs in the surrounding environment for the first time. We show that enzymes responsible for PGs formation such as cyclooxygenase, prostaglandin E synthase 2-like and prostaglandin F synthase are mainly expressed at the end of the exponential phase and that PGs are released especially during the stationary and senescent phases, suggesting a possible signaling function for these compounds. Phylogenetic analysis of the limiting enzyme, COX, indicate the presence in diatoms of more than one enzyme related to the oxidative metabolism of fatty acids belonging to the peroxidase-cyclooxygenase superfamily. These findings suggest a more complex evolution and diversity of metabolic pathways leading to the synthesis of lipid mediators in diatoms.

Pt(II) versus Pt(IV) in Carbene Glycoconjugate Antitumor Agents: Minimal Structural Variations and Great Performance Changes

Octahedral Pt(IV) complexes (2Pt-R) containing a glycoconjugate carbene ligand were prepared and fully characterized. These complexes are structural analogues to the trigonal bipyramidal Pt(II) species (1Pt-R) recently described. Thus, an unprecedented direct comparison between the biological properties of Pt compounds with different oxidation states and almost indistinguishable structural features was performed. The stability profile of the novel Pt(IV) compounds in reference solvents was determined and compared to that of the analogous Pt(II) complexes. The uptake and antiproliferative activities of 2Pt-R and 1Pt-R were evaluated on the same panel of cell lines. DNA and protein binding properties were assessed using human serum albumin, the model protein hen egg white lysozyme, and double stranded DNA model systems by a variety of experimental techniques, including UV-vis absorption spectroscopy, fluorescence, circular dichroism, and electrospray ionization mass spectrometry. Although the compounds present similar structures, their in-solution stability, cellular uptake, and DNA binding properties are diverse. These differences may represent the basis of their different cytotoxicity and biological activity.

A thermophilic C-phycocyanin with unprecedented biophysical and biochemical properties

C-phycoyanins are abundant light-harvesting pigments which have an important role in the energy transfer cascade of photosystems in prokaryotic cyanobacteria and eukaryotic red algae. These proteins have important biotechnological applications, since they can be used in food, cosmetics, nutraceutical, pharmaceutical industries and in biomedical research. Here, C-phycocyanin from the extremophilic red alga Galdieria phlegrea (GpPC) has been purified and characterized from a biophysical point of view by SDS-PAGE, mass spectrometry, UV-Vis absorption spectroscopy, circular dichroism and intrinsic fluorescence. Stability against pH variations, addition of the oxidizing agent hydrogen peroxide and the effects of temperature have been also investigated, together with its in cell antioxidant potential and antitumor activity. GpPC is stable under different pHs and unfolds at a temperature higher than 80 °C within the pH range 5.0-7.0. Its fluorescence spectra present a maximum at 650 nm, when excited at 589 nm. The protein exerts interesting in cell antioxidant properties even after high temperature treatments, like the pasteurization process, and is cytotoxic for A431 and SVT2 cancer cells, whereas it is not toxic for non-malignant cells. Our results assist in the development of C-phycocyanin as a multitasking protein, to be used in the food industry, as antioxidant and anticancer agent.

Label-free quantitative proteomics of the MCF-7 cellular response to a ferritin–metallodrug complex

Schematic summary of the experimental workflow based on label-free quantitative proteomics.

A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions

We combine fluorescence up-conversion and time correlated single photon counting experiments to investigate the 5-benzyl uracil excited state dynamics in methanol from 100 fs up to several ns. This molecule has been proposed as a model for DNA/protein interactions. Our results show emission bands at about 310 and 350 nm that exhibit bi-exponential sub-ps decays. Calculations, including solvent effects by a mixed discrete-continuum model, indicate that the Franck Condon region is characterized by significant coupling between the excited states of the benzyl and the uracil moieties, mirrored by the short-lived emission at 310 nm. Two main ground state recovery pathways are identified, both contributing to the 350 nm emission. The first 'photophysical' decay path involves a ππ* excited state localized on the uracil and is connected to the ground electronic state by an easily accessible crossing with S0, accounting for the short lifetime component. Simulations indicate that a possible second pathway is characterized by exciplex formation, with partial benzene → uracil charge transfer character, that may lead instead to photocyclization. The relevance of our results is discussed in view of the photoactivated dynamics of DNA/protein complexes, with implications on their interaction mechanisms.

A cascade extraction of active phycocyanin and fatty acids from Galdieria phlegrea

The setup of an economic and sustainable method to increase the production and commercialization of products from microalgae, beyond niche markets, is a challenge. Here, a cascade approach has been designed to optimize the recovery of high valuable bioproducts starting from the wet biomass of Galdieria phlegrea. This unicellular thermo-acidophilic red alga can accumulate high-value compounds and can live under conditions considered hostile to most other species. Extractions were performed in two sequential steps: a conventional high-pressure procedure to recover phycocyanins and a solvent extraction to obtain fatty acids. Phycocyanins were purified to the highest purification grade reported so far and were active as antioxidants on a cell-based model. Fatty acids isolated from the residual biomass contained high amount of PUFAs, more than those recovered from the raw biomass. Thus, a simple, economic, and high effective procedure was set up to isolate phycocyanin at high purity levels and PUFAs.

A Phospholipid Profile at 4 Months Predicts the Onset of Celiac Disease in at-Risk Infants

Celiac disease (CeD) is a multifactorial disease influenced by both genetic and environmental risk factors. CeD genetic components are mainly due to HLA class II genes, which account for approximately 40% of the disease heritability. The environmental factor is linked to gliadin ingestion. Despite genetic and epigenetic studies, the pathological molecular mechanism remains unclarified. The strong genetic component does not explain more than half of the hereditability; we identified several epigenetic features that contribute to the understanding of the missing hereditability. The lipid profile of infants has been proposed as a potential biomarker of CeD metabolism that can be measured before they exhibit developmental disorders and clinical symptoms. We suggest that the state of the host is a main factor for the abnormal immune response to gluten. Long before any exposure to the offending agent or any production of specific antibodies, several molecular mechanisms are differentially expressed in infants who will develop CeD compared to their peers matched for the same genetic profile. The present study explored the serum phospholipid profile of a group of infants at risk for celiac disease, followed up to 8 years to monitor the onset of CeD. We compared 30 patients who developed the disease with 20 age- and sex-matched peers with similar genetic profiles who did not develop the disease within 8 years. Serum phospholipids were analysed at 4 months, before exposure to gluten, and at 12 months of age, when none showed any marker of disease. In the 30 CeD patients, we also analysed the serum at the time of diagnosis (>24 months). The serum phospholipid profile was fairly constant across 4 and 12 months of age and, in CeD, up to 24–36 months. The phospholipid signature was dramatically different in infants who developed CeD when compared to that of control NY-CeD (Not Yet developing Celiac Disease) peers. We identified a specific serum phospholipid signature that predicts the onset of celiac disease in HLA at-risk infants years before the appearance of antibodies specific for CeD in the serum and before any clinical symptoms, even before gluten introduction into the diet at 4 months. Specifically, lysophosphatidylcholine, phosphatidylcholine, alkylacyl-phosphatidylcholine, phosphoethanolamines, phosphatidylserines, phosphatidylglycerol and phosphatidylinositol were found to be differentially represented in CeD versus NY-CeD. A set constituted by a limited number of alkylacyl-phosphatidylcholine and lyso-phosphatidylcholine, together with the duration of breast-feeding, allows the discrimination of infants who develop celiac disease before 8 years of age from those at a similar genetic risk who do not develop the disease. In addition to recent discovery, our paper unveiled a specifc phopholipid profile, able to discriminate infants who eventually develop celiac disease years before antibodies or clinical symptoms ensue.

Fiano, Greco and Falanghina grape cultivars differentiation by volatiles fingerprinting, a case study

The biomolecular characterization of edible products is gaining an increasing importance in food chemistry. The characteristic aroma or bouquet of a wine is the result of complex interactions of volatile molecules and odor receptors. Its characterization is the subject of many different studies, aimed at the development of new methods to be used for the discovery of frauds and for the typization of Protected Designation of Origin (P.D.O.) or Protected Geographic Indication (P.G.I.) wines. We previously outlined the proteomic profile of three cultivars of Vitis vinifera from South Italy (Campania) used for white wine production (Fiano, Greco and Falanghina) during the ripening. In this work, we present a mass spectrometry based study aimed at obtaining the profile of volatiles on the same samples using solid phase micro extraction coupled to gas chromatography. We demonstrated that some of the main constituents of aroma (namely terpenes, alcohols, aldehydes, etc.) were characteristic of certain grapes and absent in others.

A physicochemical investigation on the metal binding properties of TtSmtB, a thermophilic member of the ArsR/SmtB transcription factor family

The transcription factors of the ArsR/SmtB family are widespread within the bacterial and archaeal kingdoms. They are transcriptional repressors able to sense a variety of metals and undergo allosteric conformational changes upon metal binding, resulting in derepression of genes involved in detoxification. So far, the molecular determinants of specificity, selectivity, and metal binding mechanism have been scarcely investigated in thermophilic microorganisms. TtSmtB, the only ArsR/SmtB member present in the genome of Thermus thermophilus HB27, was chosen as a model to shed light into such molecular mechanisms at high temperature. In the present study, using a multidisciplinary approach, a structural and functional characterization of the protein was performed focusing on its metal interaction and chemical-physical stability. Our data demonstrate that TtSmtB has two distinct metal binding sites per monomer and interacts with di-tri-penta-valent ions with different affinity. Detailed knowledge at molecular level of protein-metal interaction is remarkable to design metal binding domains as scaffolds in metal-based therapies as well as in metal biorecovery or biosensing in the environment.

Green synthesis of conductive polyaniline by Trametes versicolor laccase using a DNA template

The green synthesis of highly conductive polyaniline by using two biological macromolecules, i.e laccase as biocatalyst, and DNA as template/dopant, was achieved in this work. Trametes versicolor laccase B (TvB) was found effective in oxidizing both aniline and its less toxic/mutagenic dimer N-phenyl-p-phenylenediamine (DANI) to conductive polyaniline. Reaction conditions for synthesis of conductive polyanilines were set-up, and structural and electrochemical properties of the two polymers were extensively investigated. When the less toxic aniline dimer was used as substrate, the polymerization reaction was faster and gave less-branched polymer. DNA was proven to work as hard template for both enzymatically synthesized polymers, conferring them a semi-ordered morphology. Moreover, DNA also acts as dopant leading to polymers with extraordinary conductive properties (∼6 S/cm). It can be envisaged that polymer properties are magnified by the concomitant action of DNA as template and dopant. Herein, the developed combination of laccase and DNA represents a breakthrough in the green synthesis of conductive materials.

Corrigendum to "Mathematical optimization of the green extraction of polyphenols from grape peels through a cyclic pressurization process" [Heliyon 5 (4) (April 2019) e01526]

[This corrects the article DOI: 10.1016/j.heliyon.2019.e01526.].

Mathematical optimization of the green extraction of polyphenols from grape peels through a cyclic pressurization process

In the current era of high consumption and increasing waste, many products that are believed to be unusable can find a new purpose in the market. For example, the grape peel waste resulting from the production of wine contains numerous bioactive compounds. In reality, grape peels are by-products of winemaking that can be conveniently reused in many different ways, including agronomic use and cosmetic industry applications. Moreover, the by-products can also be used in the energy field as biomass for the production of biogas or in food plants for the production of energy. In this article, to extract polyphenols, grape peels were processed via a cyclically pressurized extraction method known as rapid solid-liquid dynamic extraction (RSLDE), which does not require the use of any organic solvent or include heating or cooling processes that can cause the loss of substances of interest. To better understand the cyclically pressurized extraction process, a numerical simulation was performed to evaluate the exchange between the grape piece solid matrix and water during the extraction process. Furthermore, a finite element model was used to numerically determine the time-dependent concentration distribution at specific times.

Evolution of an insect immune barrier through horizontal gene transfer mediated by a parasitic wasp

Genome sequencing data have recently demonstrated that eukaryote evolution has been remarkably influenced by the acquisition of a large number of genes by horizontal gene transfer (HGT) across different kingdoms. However, in depth-studies on the physiological traits conferred by these accidental DNA acquisitions are largely lacking. Here we elucidate the functional role of Sl gasmin, a gene of a symbiotic virus of a parasitic wasp that has been transferred to an ancestor of the moth species Spodoptera littoralis and domesticated. This gene is highly expressed in circulating immune cells (haemocytes) of larval stages, where its transcription is rapidly boosted by injection of microorganisms into the body cavity. RNAi silencing of Sl gasmin generates a phenotype characterized by a precocious suppression of phagocytic activity by haemocytes, which is rescued when these immune cells are incubated in plasma samples of control larvae, containing high levels of the encoded protein. Proteomic analysis demonstrates that the protein Sl gasmin is released by haemocytes into the haemolymph, where it opsonizes the invading bacteria to promote their phagocytosis, both in vitro and in vivo. Our results show that important physiological traits do not necessarily originate from evolution of pre-existing genes, but can be acquired by HGT events, through unique pathways of symbiotic evolution. These findings indicate that insects can paradoxically acquire selective advantages with the help of their natural enemies.

Encapsulation of the Dinuclear Trithiolato-Bridged Arene Ruthenium Complex Diruthenium-1 in an Apoferritin Nanocage: Structure and Cytotoxicity

The effects of encapsulating the cytotoxic dinuclear trithiolato-bridged arene ruthenium complex [(η⁶ -p-MeC₆ H₄ iPr)₂ Ru₂ (μ₂ -S-p-C₆ H₄ tBu)₃ ]Cl (DiRu-1) within the apoferritin (AFt) nanocage were investigated. The DiRu-1-AFt nanocarrier was characterized by UV/Vis spectroscopy, ICP-MS, CD and X-ray crystallography. In contrast to previously reported Au- and Pt-based drug-loaded AFt carriers, we found no evidence of direct interactions between DiRu-1 and AFt. DiRu-1-AFt is cytotoxic toward immortalized murine BALB/c-3T3 fibroblasts transformed with SV40 virus (SVT2) and human epidermoid carcinoma A431 malignant cells, and exhibits moderate selectivity for these cancer cells over normal BALB/c-3T3 cells. DiRu-1-AFt triggers the production of reactive oxygen species, depolarization of mitochondrial membrane potential, and induces cell death via p53-mediated apoptosis. Comparison between our data and previous results suggests that the presence of specific interactions between a metal-based drug and AFt within the protein cage is not essential for drug encapsulation.

Mass spectrometry based proteomics for the molecular fingerprinting of Fiano, Greco and Falanghina cultivars

The official methodologies used for the identification and comparison of vine cultivars are ampelography and ampelometry. These methodologies are essentially based on qualitative assessments or biometric dependent morphological features of the plant. The heterogeneity of cultivars and consequently the increasing demand for a more detailed product typization, led to the introduction of new methodologies for the varietal characterization. In this scenario, proteomics has already proved to be a very useful discipline for the typization of many kinds of edible products. In this paper, we present a proteomic study carried out on three cultivars of Vitis vinifera peculiar of south Italy (Campania) used for white wine production (Fiano, Greco and Falanghina) by advanced biomolecular mass spectrometry approach. Our data highlight variations in the proteomic profiles during ripening for each cultivar and between analyzed cultivars, thus suggesting a new way to outline the biomolecular signature of vines.

FAAH-Catalyzed C-C Bond Cleavage of a New Multitarget Analgesic Drug

The discovery of extended catalytic versatilities is of great importance in both the chemistry and biotechnology fields. Fatty acid amide hydrolase (FAAH) belongs to the amidase signature superfamily and is a major endocannabinoid inactivating enzyme using an atypical catalytic mechanism involving hydrolysis of amide and occasionally ester bonds. FAAH inhibitors are efficacious in experimental models of neuropathic pain, inflammation, and anxiety, among others. We report a new multitarget drug, AGN220653, containing a carboxyamide-4-oxazole moiety and endowed with efficacious analgesic and anti-inflammatory activities, which are partly due to its capability of achieving inhibition of FAAH, and subsequently increasing the tissue concentrations of the endocannabinoid anandamide. This inhibitor behaves as a noncompetitive, slowly reversible inhibitor. Autoradiography of purified FAAH incubated with AGN220653, opportunely radiolabeled, indicated covalent binding followed by fragmentation of the molecule. Molecular docking suggested a possible nucleophilic attack by FAAH-Ser241 on the carbonyl group of the carboxyamide-4-oxazole moiety, resulting in the cleavage of the C-C bond between the oxazole and the carboxyamide moieties, instead of either of the two available amide bonds. MRM-MS analyses only detected the Ser241-assisted formation of the carbamate intermediate, thus confirming the cleavage of the aforementioned C-C bond. Quantum mechanics calculations were fully consistent with this mechanism. The study exemplifies how FAAH structural features and mechanism of action may override the binding and reactivity propensities of substrates. This unpredicted mechanism could pave the way to the future development of a completely new class of amidase inhibitors, of potential use against pain, inflammation, and mood disorders.

Preparation, structure, cytotoxicity and mechanism of action of ferritin-Pt(II) terpyridine compound nanocomposites

AIM

A Pt(II)-terpyridine compound, bearing two piperidine substituents at positions 2 and 2' of the terpyridine ligand (1), is highly cytotoxic and shows a mechanism of action distinct from cisplatin. 1 has been incorporated within the ferritin nanocage (AFt).

MATERIALS & METHODS

Spectroscopic and crystallographic data of the Pt(II)-AFt nanocomposite have been collected and in vitro anticancer activity has been explored using cancer cells.

RESULTS

Pt(II)-containing fragments bind His49, His114 and His132. Pt(II)-AFt nanocomposite is less cytotoxic than 1, but it is more toxic than cisplatin at high concentrations. The Pt(II)-AFt nanocomposite triggers necrosis in cancer cells, as free 1 does.

CONCLUSION

Pt(II)-AFt nanocomposites are promising vehicles to deliver Pt-based drugs to cancer cells.

Oxidative Stress Causes Enhanced Secretion of YB-1 Protein that Restrains Proliferation of Receiving Cells

The prototype cold-shock Y-box binding protein 1 (YB-1) is a multifunctional protein that regulates a variety of fundamental biological processes including cell proliferation and migration, DNA damage, matrix protein synthesis and chemotaxis. The plethora of functions assigned to YB-1 is strictly dependent on its subcellular localization. In resting cells, YB-1 localizes to cytoplasm where it is a component of messenger ribonucleoprotein particles. Under stress conditions, YB-1 contributes to the formation of stress granules (SGs), cytoplasmic foci where untranslated messenger RNAs (mRNAs) are sorted or processed for reinitiation, degradation, or packaging into ribonucleoprotein particles (mRNPs). Following DNA damage, YB-1 translocates to the nucleus and participates in DNA repair thereby enhancing cell survival. Recent data show that YB-1 can also be secreted and YB-1-derived polypeptides are found in plasma of patients with sepsis and malignancies. Here we show that in response to oxidative insults, YB-1 assembly in SGs is associated with an enhancement of YB-1 protein secretion. An enriched fraction of extracellular YB-1 (exYB-1) significantly inhibited proliferation of receiving cells and such inhibition was associated to a G2/M cell cycle arrest, induction of p21WAF and reduction of ΔNp63α protein level. All together, these data show that acute oxidative stress causes sustained release of YB-1 as a paracrine/autocrine signal that stimulate cell cycle arrest.

A hypothesis of sudden body fluid vaporization in the 79 AD victims of Vesuvius

In AD 79 the town of Herculaneum was suddenly hit and overwhelmed by volcanic ash-avalanches that killed all its remaining residents, as also occurred in Pompeii and other settlements as far as 20 kilometers from Vesuvius. New investigations on the victims' skeletons unearthed from the ash deposit filling 12 waterfront chambers have now revealed widespread preservation of atypical red and black mineral residues encrusting the bones, which also impregnate the ash filling the intracranial cavity and the ash-bed encasing the skeletons. Here we show the unique detection of large amounts of iron and iron oxides from such residues, as revealed by inductively coupled plasma mass spectrometry and Raman microspectroscopy, thought to be the final products of heme iron upon thermal decomposition. The extraordinarily rare preservation of significant putative evidence of hemoprotein thermal degradation from the eruption victims strongly suggests the rapid vaporization of body fluids and soft tissues of people at death due to exposure to extreme heat.

Ferritin nanocages loaded with gold ions induce oxidative stress and apoptosis in MCF-7 human breast cancer cells

Two anticancer gold(iii) compounds, Au2phen and Auoxo4, were encapsulated within a ferritin nanocage. The gold-compound loaded proteins were characterized by UV-Vis spectroscopy, inductively coupled plasma mass spectrometry and circular dichroism. X-ray crystallography shows that the compounds degrade upon encapsulation and gold(i) ions bind Ft within the cage, close to the side chains of Cys126. The gold-encapsulated nanocarriers are cytotoxic to human cancer cells. Au(i)-loaded Ft, obtained upon the encapsulation of Au2phen within the cage, induces oxidative stress activation, which finally leads to apoptosis in MCF-7 cells.