Optimisation of electrochemical sensors based on molecularly imprinted polymers: from OFAT to machine learning.

Molecularly imprinted polymers (MIPs) rely on synthetic engineered materials able to selectively bind and intimately recognise a target molecule through its size and functionalities. The way in which MIPs interact with their targets, and the magnitude of this interaction, is closely linked to the chemical properties derived during the polymerisation stages, which tailor them to their specific target. Hence, MIPs are in-deep studied in terms of their sensitivity and cross-reactivity, further being used for monitoring purposes of analytes in complex analytical samples. As MIPs are involved in sensor development within different approaches, a systematic optimisation and rational data-driven sensing is fundamental to obtaining a best-performant MIP sensor. In addition, the closer integration of MIPs in sensor development requires that the inner properties of the materials in terms of sensitivity and selectivity are maintained in the presence of competitive molecules, which focus is currently opened. Identifying computational models capable of predicting and reporting the best-performant configuration of electrochemical sensors based on MIPs is of immense importance. The application of chemometrics using design of experiments (DoE) is nowadays increasingly adopted during optimisation problems, which largely reduce the number of experimental trials. These approaches, together with the emergent machine learning (ML) tool in sensor data processing, represent the future trend in design and management of point-of-care configurations based on MIP sensing. This review provides an overview on the recent application of chemometrics tools in optimisation problems during development and analytical assessment of electrochemical sensors based on MIP receptors. A comprehensive discussion is first presented to cover the recent advancements on response surface methodologies (RSM) in optimisation studies of MIPs design. Therefore, the recent advent of machine learning in sensor data processing will be focused on MIPs development and analytical detection in sensors.

Insights into Plastic Degradation Processes in Marine Environment by X-ray Photoelectron Spectroscopy Study.

The present study employs X-ray photoelectron spectroscopy (XPS) to analyze plastic samples subjected to degradation processes with the aim to gain insight on the relevant chemical processes and disclose fragmentation mechanisms. Two model plastics, namely polystyrene (PS) and polyethylene (PE), are selected and analyzed before and after artificial UV radiation-triggered weathering, under simulated environmental hydrodynamic conditions, in fresh and marine water for different time intervals. The object of the study is to identify and quantify chemical groups possibly evidencing the occurrence of hydrolysis and oxidation reactions, which are the basis of degradation processes in the environment, determining macroplastic fragmentation. Artificially weathered plastic samples are analyzed also by Raman and FT-IR spectroscopy. Changes in surface chemistry with weathering are revealed by XPS, involving the increase in chemical moieties (hydroxyl, carbonyl, and carboxyl functionalities) which can be correlated with the degradation processes responsible for macroplastic fragmentation. On the other hand, the absence of significant modifications upon plastics weathering evidenced by Raman and FT-IR spectroscopy confirms the importance of investigating plastics surface, which represents the very first part of the materials exposed to degradation agents, thus revealing the power of XPS studies for this purpose. The XPS data on experimentally weathered particles are compared with ones obtained on microplastics collected from real marine environment for investigating the occurring degradation processes.

Age-Related Properties of Aquaponics-Derived Tilapia Skin (Oreochromis niloticus): A Structural and Compositional Study.

In the last two decades, fisheries and fish industries by-products have started to be recovered for the extraction of type I collagen because of issues related to the extraction of traditional mammalian tissues. In this work, special attention has been paid to by-products from fish bred in aquaponic plants. The valorization of aquaponic fish wastes as sources of biopolymers would make the derived materials eco-friendlier and attractive in terms of profitability and cost effectiveness. Among fish species, Nile Tilapia is the second-most farmed species in the world and its skin is commonly chosen as a collagen extraction source. However, to the best of our knowledge, no studies have been carried out to investigate, in depth, the age-related differences in fish skin with the final aim of selecting the most advantageous fish size for collagen extraction. In this work, the impact of age on the structural and compositional properties of Tilapia skin was evaluated with the aim of selecting the condition that best lends itself to the extraction of type I collagen for biomedical applications, based on the known fact that the properties of the original tissue have a significant impact on those of the final product. Performed analysis showed statistically significant age-related differences. In particular, an increase in skin thickness (+110 µm) and of wavy-like collagen fiber bundle diameter (+3 µm) besides their organization variation was observed with age. Additionally, a preferred collagen molecule orientation along two specific directions was revealed, with a higher fiber orientation degree according to age. Thermal analysis registered a shift of the endothermic peak (+1.7 °C) and an increase in the enthalpy (+3.3 J/g), while mechanical properties were found to be anisotropic, with an age-dependent brittle behavior. Water (+13%) and ash (+0.6%) contents were found to be directly proportional with age, as opposed to protein (-8%) and lipid (-10%) contents. The amino acid composition revealed a decrease in the valine, leucine, isoleucine, and threonine content and an increase in proline and hydroxyproline. Lastly, fatty acids C14:0, C15:0, C16:1, C18:2n6c, C18:3n6, C18:0, C20:3n3, and C23:0 were revealed to be upregulated, while C18:1n9c was downregulated with age.

Analysis of CGF Biomolecules, Structure and Cell Population: Characterization of the Stemness Features of CGF Cells and Osteogenic Potential.

Concentrated Growth Factors (CGF) represent new autologous (blood-derived biomaterial), attracting growing interest in the field of regenerative medicine. In this study, the chemical, structural, and biological characterization of CGF was carried out. CGF molecular characterization was performed by GC/MS to quantify small metabolites and by ELISA to measure growth factors and matrix metalloproteinases (MMPs) release; structural CGF characterization was carried out by SEM analysis and immunohistochemistry; CGF has been cultured, and its primary cells were isolated for the identification of their surface markers by flow cytometry, Western blot, and real-time PCR; finally, the osteogenic differentiation of CGF primary cells was evaluated through matrix mineralization by alizarin red staining and through mRNA quantification of osteogenic differentiation markers by real-time PCR. We found that CGF has a complex inner structure capable of influencing the release of growth factors, metabolites, and cells. These cells, which could regulate the production and release of the CGF growth factors, show stem features and are able to differentiate into osteoblasts producing a mineralized matrix. These data, taken together, highlight interesting new perspectives for the use of CGF in regenerative medicine.

Pirin: A novel redox-sensitive modulator of primary and secondary metabolism in Streptomyces.

Pirins are evolutionarily conserved iron-containing proteins that are found in all kingdoms of life, and have been implicated in diverse molecular processes, mostly associated with cellular stress. In the present study, we started from the evidence that the insertional inactivation of pirin-like gene SAM23877_RS18305 (pirA) by ΦC31 Att/Int system-based vectors in spiramycin-producing strain Streptomyces ambofaciens ATCC 23877 resulted in marked effects on central carbon and energy metabolism gene expression, high sensitivity to oxidative injury and repression of polyketide antibiotic production. By using integrated transcriptomic, proteomic and metabolite profiling, together with genetic complementation, we here show that most of these effects could be traced to the inability of the pirA-defective strain to modulate beta-oxidation pathway, leading to an unbalanced supply of precursor monomers for polyketide biosynthesis. Indeed, in silico protein-protein interaction modeling and in vitro experimental validation allowed us to demonstrate that PirA is a novel redox-sensitive negative modulator of very long-chain acyl-CoA dehydrogenase, which catalyzes the first committed step of the beta-oxidation pathway.

Comparative genomics revealed key molecular targets to rapidly convert a reference rifamycin-producing bacterial strain into an overproducer by genetic engineering.

Rifamycins are mainstay agents in treatment of many widespread diseases, but how an improved rifamycin producer can be created is still incompletely understood. Here, we describe a comparative genomic approach to investigate the mutational patterns introduced by the classical mutate-and-screen method in the genome of an improved rifamycin producer. Comparing the genome of the rifamycin B overproducer Amycolatopsis mediterranei HP-130 with those of the reference strains A. mediterranei S699 and U32, we identified 250 variations, affecting 227 coding sequences (CDS), 109 of which were HP-130-specific since they were absent in both S699 and U32. Mutational and transcriptional patterns indicated a series of genomic manipulations that not only proved the causative effect of mutB2 (coding for methylmalonyl-CoA mutase large subunit) and argS2 (coding for arginyl tRNA synthetase) mutations on the overproduction of rifamycin, but also constituted a rational strategy to genetically engineer a reference strain into an overproducer.

Rational Design of a Portable Chemometric-Assisted Voltammetric Sensor Based on Ion-Imprinted Polymeric Film for Co(II) Determination in Water.

Herein, chemometric-assisted synthesis of electrochemical sensors based on electropolymerised ion-imprinted polymeric (e-IIP) films was explored. Co(II)-IIPs sensors were prepared by performing electropolymerisation procedures of polymerisation mixtures comprising varying concentrations of an electroactive o-aminophenol (o-AP) monomer and Co(II) ions, respectively, according to the Taguchi L9 experimental design, exploiting the simultaneous evaluation of other controlled parameters during electrosynthesis. Each e-IIP developed from Taguchi runs was compared with the respective non-imprinted polymer (NIP) films and fitted according to Langmuir-Freudlich isotherms. Distinctive patterns of low and high-affinity films were screened based on the qualities and properties of the developed IIPs in terms of binding kinetics (KD), imprinting factor, and the heterogeneity index of produced cavities. These results can provide a generic protocol for chemometric-assisted synthesis of e-IIPs based on poly-o-AP, providing highly stable, reproducible, and high-affinity imprinted polymeric films for monitoring purposes.

Thiostrepton, a resurging drug inhibiting the stringent response to counteract antibiotic-resistance and expression of virulence determinants in Neisseria gonorrhoeae.

Due to the increased resistance to all available antibiotics and the lack of vaccines, Neisseria gonorrhoeae (the gonococcus) poses an urgent threat. Although the mechanisms of virulence and antibiotic resistance have been largely investigated in this bacterium, very few studies have addressed the stringent response (SR) that in pathogenic bacteria controls the expression of genes involved in host-pathogen interaction and tolerance and persistence toward antibiotics. In this study, the results of the transcriptome analysis of a clinical isolate of N. gonorrhoeae, after induction of the SR by serine hydroxamate, provided us with an accurate list of genes that are transcriptionally modulated during the SR. The list includes genes associated with metabolism, cellular machine functions, host-pathogen interaction, genome plasticity, and antibiotic tolerance and persistence. Moreover, we found that the artificial induction of the SR in N. gonorrhoeae by serine hydroxamate is prevented by thiostrepton, a thiopeptide antibiotic that is known to interact with ribosomal protein L11, thereby inhibiting functions of EF-Tu and EF-G, and binding of pppGpp synthase I (RelA) to ribosome upon entry of uncharged tRNA. We found that N. gonorrhoeae is highly sensitive to thiostrepton under in vitro conditions, and that thiostrepton, in contrast to other antibiotics, does not induce tolerance or persistence. Finally, we observed that thiostrepton attenuated the expression of key genes involved in the host-pathogen interaction. These properties make thiostrepton a good drug candidate for dampening bacterial virulence and preventing antibiotic tolerance and persistence. The ongoing challenge is to increase the bioavailability of thiostrepton through the use of chemistry and nanotechnology.

Particle uptake by filter-feeding macrofoulers from the Mar Grande of Taranto (Mediterranean Sea, Italy): potential as microplastic pollution bioremediators.

Microplastics (MPs) are a serious threat to the marine environment affecting ecosystem functioning and biodiversity. There is a vast literature about the uptake of MPs at different trophic levels, mainly focused on ecotoxicological effects in commercially relevant species. Little is still known about possible strategies to face MP pollution. Bioremediation is recently gaining attention in this framework. The clearance rate and particle retention of Sabella spallanzanii, Mytilus galloprovincialis, Phallusia mammillata, Paraleucilla magna at three MP concentrations (C1: 1.4 · 101 p/L; C2: 1.4 · 102 p/L; C3: 1.4 · 103 p/L) were investigated to test their potential as MP remover. Digestion protocol removed 98 % of tissues simplifying the MP quantification. P. magna clearance rate decreased with increasing concentration while P. mammillata showed no significant variations. S. spallanzanii and M. galloprovincialis instead exhibited the highest values of clearance rate. Yet, unlike mussels, S. spallanzanii can inhibit particle return to the surrounding water storing them in the tube, resulting to be the best candidate for bioremediation purposes.

Interplay between non-coding RNA transcription, stringent phenotype and antibiotic production in Streptomyces.

While in recent years the key role of non-coding RNAs (ncRNAs) in regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces, and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: i.) the wild type strain; ii.) an isogenic pirA-defective mutant with central carbon metabolism imbalance, "relaxed" phenotype, and repression of antibiotic production; iii.) a pirA-derivative strain harboring a "stringent" RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.

Aquaponics-Derived Tilapia Skin Collagen for Biomaterials Development.

Collagen is one of the most widely used biomaterials in health-related sectors. The industrial production of collagen mostly relies on its extraction from mammals, but several issues limited its use. In the last two decades, marine organisms attracted interest as safe, abundant, and alternative source for collagen extraction. In particular, the possibility to valorize the huge quantity of fish industry waste and byproducts as collagen source reinforced perception of fish collagen as eco-friendlier and particularly attractive in terms of profitability and cost-effectiveness. Especially fish byproducts from eco-sustainable aquaponics production allow for fish biomass with additional added value and controlled properties over time. Among fish species, Oreochromis niloticus is one of the most widely bred fish in large-scale aquaculture and aquaponics systems. In this work, type I collagen was extracted from aquaponics-raised Tilapia skin and characterized from a chemical, physical, mechanical, and biological point of view in comparison with a commercially available analog. Performed analysis confirmed that the proprietary process optimized for type I collagen extraction allowed to isolate pure native collagen and to preserve its native conformational structure. Preliminary cellular studies performed with mouse fibroblasts indicated its optimal biocompatibility. All data confirmed the eligibility of the extracted Tilapia-derived native type I collagen as a biomaterial for healthcare applications.

Bioactive Potential of Two Marine Picocyanobacteria Belonging to Cyanobium and Synechococcus Genera.

Coccoid cyanobacteria produce a great variety of secondary metabolites, which may have useful properties, such as antibacterial, antiviral, anticoagulant or anticancer activities. These cyanobacterial metabolites have high ecological significance, and they could be considered responsible for the widespread occurrence of these microorganisms. Considering the great benefit derived from the identification of competent cyanobacteria for the extraction of bioactive compounds, two strains of picocyanobacteria (coccoid cyanobacteria < 3 µm) (Cyanobium sp. ITAC108 and Synechococcus sp. ITAC107) isolated from the Mediterranean sponge Petrosia ficiformis were analyzed. The biological effects of organic and aqueous extracts from these picocyanobacteria toward the nauplii of Artemia salina, sea urchin embryos and human cancer lines (HeLa cells) were evaluated. Methanolic and aqueous extracts from the two strains strongly inhibited larval development; on the contrary, in ethyl acetate and hexane extracts, the percentage of anomalous embryos was low. Moreover, all the extracts of the two strains inhibited HeLa cell proliferation, but methanol extracts exerted the highest activity. Gas chromatography-mass spectrometry analysis evidenced for the first time the presence of ß-N-methylamino-l-alanine and microcystin in these picocyanobacteria. The strong cytotoxic activity observed for aqueous and methanolic extracts of these two cyanobacteria laid the foundation for the production of bioactive compounds of pharmacological interest.

Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens.

While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, "relaxed" phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a "stringent" RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.

Response Surface Methodology for the Optimisation of Electrochemical Biosensors for Heavy Metals Detection.

Herein, we report the application of a chemometric tool for the optimisation of electrochemical biosensor performances. The experimental design was performed based on the responses of an amperometric biosensor developed for metal ions detection using the flow injection analysis. The electrode preparation and the working conditions were selected as experimental parameters, and thus, were modelled by a response surface methodology (RSM). In particular, enzyme concentration, flow rates, and number of cycles were reported as continuous factors, while the sensitivities of the biosensor (S, µA·mM-1) towards metals, such as Bi3+ and Al3+ were collected as responses and optimised by a central composite design (CCD). Bi3+ and Al3+ inhibition on the Pt/PPD/GOx biosensor response is for the first time reported. The optimal enzyme concentration, scan cycles and flow rate were found to be 50 U·mL-1, 30 and, 0.3 mL·min-1, respectively. Descriptive/predictive performances are discussed: the sensitivities of the optimised biosensor agreed with the experimental design prediction. The responses under the optimised conditions were also tested towards Ni2+ and Ag⁺ ions. The multivariate approach used in this work allowed us to obtain a wide working range for the biosensor, coupled with a high reproducibility of the response (RSD = 0.72%).

Characterization of two Pantoea strains isolated from extra-virgin olive oil.

The olive oil is an unfavorable substrate for microbial survival and growth. Only few microorganisms use olive oil fatty acids as carbon and energy sources, and survive in the presence of olive oil anti-microbial components. In this study, we have evaluated the occurrence of microorganisms in 1-year-stored extra-virgin olive oil samples. We detected the presence of bacterial and yeast species with a recurrence of the bacterium Stenotrophomonas rhizophila and yeast Sporobolomyces roseus. We then assayed the ability of all isolates to grow in a mineral medium supplemented with a commercial extra-virgin olive oil as a sole carbon and energy source, and analyzed the utilization of olive oil fatty acids during their growth. We finally focused on two bacterial isolates belonging to the species Pantoea septica. Both these isolates produce carotenoids, and one of them synthesizes bioemulsifiers enabling the bacteria to better survive/growth in this unfavorable substrate. Analyses point to a mixture of glycolipids with glucose, galactose and xylose as carbohydrate moieties whereas the lipid domain was constituted by C6-C10 ß-hydroxy carboxylic acids.

A multi-analytical approach for the assessment of the provenience of geological amber: the collection of the Earth Sciences Museum of Bari (Italy).

The Earth Sciences Museum of the University of Bari Aldo Moro (Italy) exhibits a wide collection of amber samples. These have been catalogued as Baltic amber (succinite), Sicilian amber (simetite), amber from New Jersey, Apennine amber and New Zealand copaline. However, some samples revealed to be erroneously classified as a consequence of incorrect information on the labels or in the museum catalogue. This may be due to historical forgeries, as is often the case of simetite, or to a possible exchange of samples that probably occurred during the displacement of the museum collection from the Central University Building to the Geo-environmental and Earth Sciences Department. In this study, all amber samples were systematically investigated with long wave UV rays, attenuated total reflectance (ATR), Fourier transform infrared (FTIR) spectroscopy and pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) using on-line thermally assisted hydrolysis and methylation. The combined use of the latter two analytical techniques allowed for a complete characterisation of the ambers, whereas UV fluorescence showed to be of little value. The compositional data could be used for a better classification and valorisation of the amber samples of the museum collection. Two of the purported amber samples were shown to be copal, while four others are ambers but had been wrongly classified. Moreover, for some samples, it could be established that they had been subjected to treatment with a drying oil.

Portable gliadin-immunochip for contamination control on the food production chain.

Celiac disease (CD) is one of the most common digestive disorders caused by an abnormal immune reaction to gluten. So far there are no available therapies, the only solution is a strict gluten-free diet, which however could be very challenging as gluten can be hidden in many food products. Furthermore an additional problem is related to cross-contamination of nominal gluten-free foods with gluten-based ones during manufacturing. Here we propose a lab on chip platform as a powerful tool to help food manufacturers to evaluate the real amount of gluten in their products by an accurate in-situ control of the production chain and maybe to specify the real gluten content in packages labeling. Our portable gliadin-immunochips, based on an electrochemical impedance spectroscopy transduction method, were first calibrated and then validated for both liquid and solid food matrixes by analyzing different beers and flours. The high specificity of our assay was also demonstrated by performing control experiments on rice and potatoes flours containing prolamin-like proteins. We achieved limit of quantification of 0.5 ppm for gliadin that is 20 times lower than the worldwide limit established for gluten-free food while the method of analysis is faster and cheaper than currently employed ELISA-based methods. Moreover our results on food samples were validated through a mass spectrometry standard analysis.

A rapid and simple method for the determination of 3,4-dihydroxyphenylacetic acid, norepinephrine, dopamine, and serotonin in mouse brain homogenate by HPLC with fluorimetric detection.

A fast and simple isocratic high-performance liquid chromatography method for the determination of 3,4-dihydroxyphenylacetic acid (DOPAC), norepinephrine (NE), dopamine (DA), and serotonin (5-HT) in homogenate samples of mouse striatum employing the direct fluorescence of the neurotransmitters is described. The method has been optimized and validated. The analytes were separated in 15min on a reversed-phase column (C18) with acetate buffer (pH 4.0, 12mM)-methanol (86:14, v/v) as mobile phase; the flow rate was 1ml/min. The fluorescence measurements were carried out at 320nm with excitation at 279nm. The calibration curve for DA was linear up to about 2.5µg/ml, with a coefficient of determination (r(2)) of 0.9995 with a lower limit of quantification of 0.031µg/ml. Since the procedure does not involve sample pre-purification or derivatisation, the recovery ranged from 97% to 102% and relative standard deviation (RSD) was better than 2.9%, the use of the internal standard is not mandatory, further simplifying the method. Similar performance was obtained for the other analytes. As a result, thanks to its simplicity, rapidity and adequate working range, the method can be used for the determination of 3,4-dihydroxyphenylacetic acid, dopamine, norepinephrine and serotonin in animal tissues. An experimental 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine mouse model of Parkinson-like disease has been used to demonstrate the method is fit-for-purpose.