Trophic ecology of Angolan cold-water coral reefs (SE Atlantic) based on stable isotope analyses.

Cold-water coral (CWC) reefs of the Angolan margin (SE Atlantic) are dominated by Desmophyllum pertusum and support a diverse community of associated fauna, despite hypoxic conditions. In this study, we use carbon and nitrogen stable isotope analyses (δ13C and δ15N) to decipher the trophic network of this relatively unknown CWC province. Although fresh phytodetritus is available to the reef, δ15N signatures indicate that CWCs (12.90 ± 1.00 ‰) sit two trophic levels above Suspended Particulate Organic Matter (SPOM) (4.23 ± 1.64 ‰) suggesting that CWCs are highly reliant on an intermediate food source, which may be zooplankton. Echinoderms and the polychaete Eunice norvegica occupy the same trophic guild, with high δ13C signatures (-14.00 ± 1.08 ‰) pointing to a predatory feeding behavior on CWCs and sponges, although detrital feeding on 13C enriched particles might also be important for this group. Sponges presented the highest δ15N values (20.20 ± 1.87 ‰), which could be due to the role of the sponge holobiont and bacterial food in driving intense nitrogen cycling processes in sponges' tissue, helping to cope with the hypoxic conditions of the reef. Our study provides first insights to understand trophic interactions of CWC reefs under low-oxygen conditions.

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.

New Evidence on the Reliable Use of Stable Isotopes of Bitumen Fractions in Archaeological Research.

One of the goals of archaeological studies is to determine how material goods and ideas moved among human populations, and bitumen is a worthy proxy because it has been used since prehistory. As a result, when bitumen is excavated from archaeological sites, determining its provenance is important because it sheds light on the trade and communication of populations at a given time. During the study of archaeological bitumen from coastal sites in central and southern Puglia (Italy), we observed that stable isotope ratios of saturated and aromatic fractions were incompatible with those obtained from asphaltenes, supporting the absorption of a foreign substance. Experiments showed that lipids are absorbed by bitumen and, in the case of oils, are distributed mainly in the saturated and aromatic fractions as their isotopic ratios change. The same experiments showed that the isotopic ratios of the asphaltenes do not change. Lipid absorption on the archaeological bitumen may have occurred before the bitumen was applied to the pottery, during the use of the pottery or while underground, before being excavated. These hypotheses are discussed, and it is concluded that the isotopic ratio of asphaltenes is a reliable proxy for provenance, whereas those of the saturated and aromatic fractions should be considered with caution due to possible lipid absorption. Nevertheless, they provide new information on pottery use that can be used in archaeological chemistry.

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.

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.

Interaction of Copper Trafficking Proteins with the Platinum Anticancer Drug Kiteplatin.

The interaction of metallodrugs with proteins influences their mechanism of action and side effects. In the case of platinum drugs, copper transporters modulate sensitivity and resistance to these anticancer agents. To deepen the knowledge of the structural properties underlying the reactivity of platinum drugs with copper transporters, we studied the interaction of kiteplatin and two of its derivatives with the methionine-rich motif of copper importer Ctr1 and with the dithiol motif of the first domain of Menkes ATPase. Furthermore, cellular uptake and cytotoxicity of the three complexes were evaluated in cisplatin-sensitive and -resistant ovarian cancer cells, comparing the data with those of clinically relevant drugs. Reactivity depends on the tightness of the chelate ring formed by the carrier ligands and the nature of the leaving and entering groups. The results highlight the importance of subtle changes in the platinum coordination sphere that affect drug absorption and intracellular fate.

Optimization of a new multi-reagent procedure for quantitative mussel digestion in microplastic analysis.

Over the last few years, different digestion protocols have been proposed to extract microplastics from mussels, an important product from aquaculture and a relevant economic resource, always scrutinized as a potential pollutant concentrator. In this study, a full factorial experimental design technique has been employed to achieve efficiency in removing biological materials while maximizing the recoveries of five common microplastics (polyethylene, polystyrene, polyethylene terephthalate, polypropylene and polyamide). A robust setpoint was calculated, 2.5% potassium hydroxide at 60 °C for 3 h with 5% hydrogen peroxide and 2.7% of methanol, permitting the quantitative digestion of mussel tissues and recovery of microplastics. These experimental conditions were successfully used to digest whole mussels bought from a local market, which possess high levels of microplastic contamination (41 items/g dry weight). The results highlight the importance of optimizing protocols to develop robust, easy to use and cheap quantitative approaches for analysing microplastic accumulation in edible organisms.

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.

Directional Immobilization of Proteins on Gold Nanoparticles Is Essential for Their Biological Activity: Leptin as a Case Study.

Gold nanomaterials hold great potential for biomedical applications. While this field is evolving rapidly, little attention has been paid to precise nanoparticle design and functionalization. Here, we show that when using proteins as targeting moieties, it is fundamental to immobilize them directionally to preserve their biological activity. Using full-length leptin as a case study, we have developed two alternative conjugation strategies for protein immobilization based on either a site-selective or a nonselective derivatization approach. We show that only nanoparticles with leptin immobilized site-selectively fully retain the ability to interact with the cognate leptin receptor. These results demonstrate the importance of a specified molecular design when preparing nanoparticles labeled with proteins.

Easy fabrication of mussel inspired coated foam and its optimization for the facile removal of copper from aqueous solutions.

Herein we present a straightforward approach for the use of polydopamine (PDA) in adsorption of heavy metals from aqueous solutions. This is achieved by fabricating a healthy and environmentally friendly polydimethylsiloxane (PDMS) foam with a mussel inspired PDA layer deposited on the surface. Critical adsorption parameters (pH, temperature and PDA thickness) are optimized by the application of experimental design methodology. Adsorption kinetics and isotherms are studied in detail evidencing a good fitting with Langmuir isotherm and pseudo-second-order kinetics thus suggesting the occurrence of a chemical sorption process with monolayer nature between metals and PDMS/PDA foam. Intraparticle diffusion model evidences good accessibility and high affinity of binding sites on PDA surface. Once adsorbed, metals are reduced to a lower toxic form and can be then removed by a mild acidic treatment thus being easily collected and stocked.

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%).

Accumulation of endocrine disrupting chemicals in the liver of Diplodus sargus sargus in Torre Guaceto Natural Reserve.

Studies on the quality of marine environments in Italy have traditionally favoured heavily impacted areas, such as harbours and industrial areas, while there are few investigations aimed at the evaluation of the presence of organic pollutants in the areas of marine reserve. The aim of this study was to determine endocrine-disrupting compounds (EDCs) in the liver of white seabreams (Diplodus sargus sargus) from the Natural Reserve of Torre Guaceto, Italy. Among EDCs, alkyl-phenols 2,6-DTBP, 2,4-DTBP, OP, and BPA were identified and quantified. The mean concentration of 2,6-DTBP, 2,4-DTBP, OP, and BPA were 2.2, 2.0, 1.2 and 3.6ng/g of liver, respectively, confirming the occurrence and transfer of these organic pollutants in the food web of marine organisms in marine reserves.

Bioanalytical Application of Amino Acid Detection by Capillary Electrophoresis.

This chapter illustrates the usefulness of capillary electrophoresis (CE) for the analysis of amino acids, and both normal and chiral separations are covered. In order to provide a general description of the main results and challenges in the biomedical field, some relevant applications and reviews on CE of amino acids are tabulated. Furthermore, some detailed experimental procedures are shown, regarding the CE analysis of amino acids in body fluids, in microdialysate, and released upon hydrolysis of proteins. In particular, the protocols will deal with the following compounds: (1) underivatized aminoacids in blood; (2) γ-Aminobutyric acid, glutamate, and L-Aspartate derivatized with Naphthalene-2,3-dicarboxaldehyde; (3) hydrolysate from bovine serum albumine derivatized with phenylisothiocyanate. By examining these applications on real matrices, the capillary electrophoresis efficiency as tool for Amino Acid analysis can be ascertained.

Characterization of Human and Yeast Mitochondrial Glycine Carriers with Implications for Heme Biosynthesis and Anemia.

Heme is an essential molecule in many biological processes, such as transport and storage of oxygen and electron transfer as well as a structural component of hemoproteins. Defects of heme biosynthesis in developing erythroblasts have profound medical implications, as represented by sideroblastic anemia. The synthesis of heme requires the uptake of glycine into the mitochondrial matrix where glycine is condensed with succinyl coenzyme A to yield δ-aminolevulinic acid. Herein we describe the biochemical and molecular characterization of yeast Hem25p and human SLC25A38, providing evidence that they are mitochondrial carriers for glycine. In particular, the hem25Δ mutant manifests a defect in the biosynthesis of δ-aminolevulinic acid and displays reduced levels of downstream heme and mitochondrial cytochromes. The observed defects are rescued by complementation with yeast HEM25 or human SLC25A38 genes. Our results identify new proteins in the heme biosynthetic pathway and demonstrate that Hem25p and its human orthologue SLC25A38 are the main mitochondrial glycine transporters required for heme synthesis, providing definitive evidence of their previously proposed glycine transport function. Furthermore, our work may suggest new therapeutic approaches for the treatment of congenital sideroblastic anemia.

New evidences on efficacy of boronic acid-based derivatization method to identify sugars in plant material by gas chromatography-mass spectrometry.

This work presents an analytical procedure based on gas chromatography-mass spectrometry which allows the determination of aldoses (glucose, mannose, galactose, arabinose, xylose, fucose, rhamnose) and chetoses (fructose) in plant material. One peak for each target carbohydrate was obtained by using an efficient derivatization employing methylboronic acid and acetic anhydride sequentially, whereas the baseline separation of the analytes was accomplished using an ionic liquid capillary column. First, the proposed method was optimized and validated. Successively, it was applied to identify the carbohydrates present in plant material. Finally, the procedure was successfully applied to samples from a XVII century painting, thus highlighting the occurrence of starch glue and fruit tree gum as polysaccharide materials.

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.

Within-otolith variability in chemical fingerprints: implications for sampling designs and possible environmental interpretation.

Largely used as a natural biological tag in studies of dispersal/connectivity of fish, otolith elemental fingerprinting is usually analyzed by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). LA-ICP-MS produces an elemental fingerprint at a discrete time-point in the life of a fish and can generate data on within-otolith variability of that fingerprint. The presence of within-otolith variability has been previously acknowledged but not incorporated into experimental designs on the presumed, but untested, grounds of both its negligibility compared to among-otolith variability and of spatial autocorrelation among multiple ablations within an otolith. Here, using a hierarchical sampling design of spatial variation at multiple scales in otolith chemical fingerprints for two Mediterranean coastal fishes, we explore: 1) whether multiple ablations within an otolith can be used as independent replicates for significance tests among otoliths, and 2) the implications of incorporating within-otolith variability when assessing spatial variability in otolith chemistry at a hierarchy of spatial scales (different fish, from different sites, at different locations on the Apulian Adriatic coast). We find that multiple ablations along the same daily rings do not necessarily exhibit spatial dependency within the otolith and can be used to estimate residual variability in a hierarchical sampling design. Inclusion of within-otolith measurements reveals that individuals at the same site can show significant variability in elemental uptake. Within-otolith variability examined across the spatial hierarchy identifies differences between the two fish species investigated, and this finding leads to discussion of the potential for within-otolith variability to be used as a marker for fish exposure to stressful conditions. We also demonstrate that a 'cost'-optimal allocation of sampling effort should typically include some level of within-otolith replication in the experimental design. Our findings provide novel evidence to aid the design of future sampling programs and improve our general understanding of the mechanisms regulating elemental fingerprints.

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.

Dispersal patterns of coastal fish: implications for designing networks of marine protected areas.

Information about dispersal scales of fish at various life history stages is critical for successful design of networks of marine protected areas, but is lacking for most species and regions. Otolith chemistry provides an opportunity to investigate dispersal patterns at a number of life history stages. Our aim was to assess patterns of larval and post-settlement (i.e. between settlement and recruitment) dispersal at two different spatial scales in a Mediterranean coastal fish (i.e. white sea bream, Diplodus sargus sargus) using otolith chemistry. At a large spatial scale (∼200 km) we investigated natal origin of fish and at a smaller scale (∼30 km) we assessed "site fidelity" (i.e. post-settlement dispersal until recruitment). Larvae dispersed from three spawning areas, and a single spawning area supplied post-settlers (proxy of larval supply) to sites spread from 100 to 200 km of coastline. Post-settlement dispersal occurred within the scale examined of ∼30 km, although about a third of post-settlers were recruits in the same sites where they settled. Connectivity was recorded both from a MPA to unprotected areas and vice versa. The approach adopted in the present study provides some of the first quantitative evidence of dispersal at both larval and post-settlement stages of a key species in Mediterranean rocky reefs. Similar data taken from a number of species are needed to effectively design both single marine protected areas and networks of marine protected areas.