Biochemical characterization of a new mitochondrial transporter of dephosphocoenzyme A in Drosophila melanogaster.

CoA is an essential cofactor that holds a central role in cell metabolism. Although its biosynthetic pathway is conserved across the three domains of life, the subcellular localization of the eukaryotic biosynthetic enzymes and the mechanism behind the cytosolic and mitochondrial CoA pools compartmentalization are still under debate. In humans, the transport of CoA across the inner mitochondrial membrane has been ascribed to two related genes, SLC25A16 and SLC25A42 whereas in D. melanogaster genome only one gene is present, CG4241, phylogenetically closer to SLC25A42. CG4241 encodes two alternatively spliced isoforms, dPCoAC-A and dPCoAC-B. Both isoforms were expressed in Escherichia coli, but only dPCoAC-A was successfully reconstituted into liposomes, where transported dPCoA and, to a lesser extent, ADP and dADP but not CoA, which was a powerful competitive inhibitor. The expression of both isoforms in a Saccharomyces cerevisiae strain lacking the endogenous putative mitochondrial CoA carrier restored the growth on respiratory carbon sources and the mitochondrial levels of CoA. The results reported here and the proposed subcellular localization of some of the enzymes of the fruit fly CoA biosynthetic pathway, suggest that dPCoA may be synthesized and phosphorylated to CoA in the matrix, but it can also be transported by dPCoAC to the cytosol, where it may be phosphorylated to CoA by the monofunctional dPCoA kinase. Thus, dPCoAC may connect the cytosolic and mitochondrial reactions of the CoA biosynthetic pathway without allowing the two CoA pools to get in contact.

UCP2 transports C4 metabolites out of mitochondria, regulating glucose and glutamine oxidation.

Uncoupling protein 2 (UCP2) is involved in various physiological and pathological processes such as insulin secretion, stem cell differentiation, cancer, and aging. However, its biochemical and physiological function is still under debate. Here we show that UCP2 is a metabolite transporter that regulates substrate oxidation in mitochondria. To shed light on its biochemical role, we first studied the effects of its silencing on the mitochondrial oxidation of glucose and glutamine. Compared with wild-type, UCP2-silenced human hepatocellular carcinoma (HepG2) cells, grown in the presence of glucose, showed a higher inner mitochondrial membrane potential and ATP:ADP ratio associated with a lower lactate release. Opposite results were obtained in the presence of glutamine instead of glucose. UCP2 reconstituted in lipid vesicles catalyzed the exchange of malate, oxaloacetate, and aspartate for phosphate plus a proton from opposite sides of the membrane. The higher levels of citric acid cycle intermediates found in the mitochondria of siUCP2-HepG2 cells compared with those found in wild-type cells in addition to the transport data indicate that, by exporting C4 compounds out of mitochondria, UCP2 limits the oxidation of acetyl-CoA-producing substrates such as glucose and enhances glutaminolysis, preventing the mitochondrial accumulation of C4 metabolites derived from glutamine. Our work reveals a unique regulatory mechanism in cell bioenergetics and provokes a substantial reconsideration of the physiological and pathological functions ascribed to UCP2 based on its purported uncoupling properties.

Airborne asbestos fibres monitoring in tunnel excavation.

Tunnelling across ophiolitic formation with Naturally Occurring Asbestos (NOA) can release fibres into the environment, exposing workers, and the population, if fibres spread outside the tunnel, leading to increased risk of developing asbestos-related disease. Therefore, a careful plan of environmental monitoring is carried out during Terzo Valico tunnel excavation. In the present study, data of 1571 samples of airborne dust, collected between 2014 and 2016 inside the tunnels, and analyzed by SEM-EDS for quantification of workers exposure, are discussed. In particular, the engineering and monitoring management of 100 m tunnelling excavation across a serpentinite lens (Cravasco adit), intercalated within calcschists, is reported. At this chrysotile occurrence, 84% of 128 analyzed samples (from the zone closer to the front rock) were above 2 ff/l. However, thanks to safety measures implemented and tunnel compartmentation in zones, the asbestos fibre concentration did not exceed the Italian standard of occupational exposure (100 ff/l) and 100% of samples collected in the outdoor square were below 1 ff/l. During excavation under normal working conditions, asbestos concentrations were below 2 ff/l in 97.4% of the 668 analyzed samples. Our results showed that air monitoring can objectively confirm the presence of asbestos minerals at a rock front in relative short time and provide information about the nature of the lithology at the front. The present dataset, the engineering measures described and the operative conclusions are liable to support the improvement of legislation on workers exposure to asbestos referred to the tunnelling sector, lacking at present.

Distance-dependent hydrophobic-hydrophobic contacts in protein folding simulations.

Successful prediction of protein folding from an amino acid sequence is a challenge in computational biology. In order to reveal the geometric constraints that drive protein folding, highlight those constraints kept or missed by distinct lattices and for establishing which class of intra- and inter-secondary structure element interactions is the most relevant for the correct folding of proteins, we have calculated inter-alpha carbon distances in a set of 42 crystal structures consisting of mainly helix, sheet or mixed conformations. The inter-alpha carbon distances were also calculated in several lattice "hydrophobic-polar" models built from the same protein set. We found that helix structures are more prone to form "hydrophobic-hydrophobic" contacts than beta-sheet structures. At a distance lower than or equal to 3.8 Å (very short-range interactions), "hydrophobic-hydrophobic" contacts are almost absent in the native structures, while they are frequent in all the analyzed lattice models. At distances in-between 3.8 and 9.5 Å (short-/medium-range interactions), the best performing lattice for reproducing mainly helix structures is the body-centered-cubic lattice. If protein structures contain sheet portions, lattice performances get worse, with few exceptions observed for double-tetrahedral and body-centered-cubic lattices. Finally, we can observe that ab initio protein folding algorithms, i.e. those based on the employment of lattices and Monte Carlo simulated annealings, can be improved simply and effectively by preventing the generation of "hydrophobic-hydrophobic" contacts shorter than 3.8 Å, by monitoring the "hydrophobic-hydrophobic/polar-polar" contact ratio in short-/medium distance ranges and by using preferentially a body-centered-cubic lattice.

Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening.

The functional characterization of proteins represents a daily challenge for biochemical, medical and computational sciences. Although finally proved on the bench, the function of a protein can be successfully predicted by computational approaches that drive the further experimental assays. Current methods for comparative modeling allow the construction of accurate 3D models for proteins of unknown structure, provided that a crystal structure of a homologous protein is available. Binding regions can be proposed by using binding site predictors, data inferred from homologous crystal structures, and data provided from a careful interpretation of the multiple sequence alignment of the investigated protein and its homologs. Once the location of a binding site has been proposed, chemical ligands that have a high likelihood of binding can be identified by using ligand docking and structure-based virtual screening of chemical libraries. Most docking algorithms allow building a list sorted by energy of the lowest energy docking configuration for each ligand of the library. In this review the state-of-the-art of computational approaches in 3D protein comparative modeling and in the study of protein-ligand interactions is provided. Furthermore a possible combined/concerted multistep strategy for protein function prediction, based on multiple sequence alignment, comparative modeling, binding region prediction, and structure-based virtual screening of chemical libraries, is described by using suitable examples. As practical examples, Abl-kinase molecular modeling studies, HPV-E6 protein multiple sequence alignment analysis, and some other model docking-based characterization reports are briefly described to highlight the importance of computational approaches in protein function prediction.

A new Caucasian case of neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD): a clinical, molecular, and functional study.

Citrin is the liver-specific isoform of the mitochondrial aspartate/glutamate carrier (AGC2). AGC2 deficiency is an autosomal recessive disorder with two age related phenotypes: neonatal intrahepatic cholestasis (NICCD, OMIM#605814) and adult-onset type II citrullinemia (CTLN2, OMIM#603471). NICCD arises within the first few weeks of life resulting in prolonged cholestasis and metabolic abnormalities including aminoacidemia and galactosuria. Usually symptoms disappear within the first year of life, thus making a diagnosis difficult after this time. In this study we report a new Caucasian case of NICCD, a seven week old Romanian boy with prolonged jaundice. Sequencing of the AGC2 gene showed a novel homozygous missense double-nucleotide (doublet) mutation, which produces the change of the glycine at position 437 into glutamate. Functional studies, carried out on the recombinant mutant protein, for the first time demonstrated, that NICCD is caused by a reduced transport activity of AGC2. The presence of AGC2 deficiency in other ethnic groups besides Asian population suggests further consideration for NICCD diagnosis of any neonate with an unexplained cholestasis; a prompt diagnosis is crucial to resolve the metabolic decompensation with an appropriate dietary treatment.

Trans-Chalcone prevents VEGF expression and retinal neovascularization in the ischemic retina.

Retinal neovascularization (RNV) is a critical pathological event and a major cause of blindness. Vascular inflammation and oxidative stress have been shown to play a key role in the induction and progression of RNV. Trans-Chalcone-derived flavonoids have been previously shown to be negative modulators of oxidative stress and inflammatory responses as well as tumor angiogenesis. In this study, we characterized the effects of the flavonoid trans-Chalcone in preventing RNV in a model of ischemic retinopathy. Ischemic retinopathy was induced in neonatal mice subjected to oxygen-induced retinopathy. Trans-Chalcone was administered intra-peritoneum at the dose of 25 mg/kg/day. Vascular density was assessed by morphometric analysis of flat mounted retinas stained with Texas red-Isolectin B4. Western blotting analysis was conducted to determine protein levels of vascular endothelial growth factor (VEGF), inter-cellular adhesion molecule 1 (ICAM-1) and the transcriptional activators' signal transducer and activator of transcription 3 (STAT3) and nuclear factor kappa beta (NF-κB). Treatment with trans-Chalcone significantly inhibited RNV in the ischemic retina, as shown by decreased number of neovascular tufts. Trans-Chalcone also blocked ischemia-induced VEGF and ICAM-1 expression and this effect correlated with inhibition of activated STAT3 and NF-κB. Our results show that trans-Chalcone effectively prevents RNV in the murine retina thus suggesting that Chalcone-derived flavonoids may be beneficial in preventing pathological neovascularization in the ischemic retina.

Dispersion of Natural Airborne TiO2 Fibres in Excavation Activity as a Potential Environmental and Human Health Risk.

Titanium is the ninth most abundant element, approximately 0.7% of the Earth crust. It is used worldwide in large quantities for various applications. The IARC includes TiO2 in Group 2B as possibly carcinogenic to humans suggesting that pathological effects correlate to particle size and shape. This study case quantifies the release of natural TiO2 particles during mining activity, involving meta-basalt and shale lithologies in the Ligurian Alps, during excavation of the Terzo Valico as part of the Trans-European Transport Network. Type, width, length, aspect ratio, and concentration of TiO2 particles in needle habit were determined. The different samplings have reported that airborne concentrations in meta-basalt were 4.21 ff/L and 23.94 ff/L in shale. In both cases, the concentration never exceeds the limits established by various organizations for workers health protection. Nevertheless, TiO2 elongated particles, recognized as rutile, showed the dimensional characteristic of fibres, as reported by WHO. These fibres deserve particular attention because they can reach the alveolar space and trigger inflammation and chronic diseases. The results indicate that monitoring the TiO2 in both working environments and Ti-rich geological formations, associated with epidemiological studies, may represent a useful tool to determine the exposure risk of workers and the general population.

Molecular modeling of antibodies for the treatment of TNFα-related immunological diseases.

Therapeutic monoclonal antibodies (mAbs) have high efficacy in treating TNF α-related immunological diseases. Other than neutralizing TNF α, these IgG1 antibodies exert Fc receptor-mediated effector functions such as the complement-dependent cytotoxicity (CDC) and antibody-dependent cell cytotoxicity (ADCC). The crystallizable fragment (Fc) of these IgG1 contains a single glycosylation site at Asn 297/300 that is essential for the CDC and ADCC. Glycosylated antibodies lacking core fucosylation showed an improved ADCC. However, no structural data are available concerning the ligand-binding interaction of these mAbs used in TNF α-related diseases and the role of the fucosylation. We therefore used comparative modeling for generating complete 3D mAb models that include the antigen-binding fragment (Fab) portions of infliximab, complexed with TNF α (4G3Y.pdb), the Fc region of the human IGHG1 fucosylated (3SGJ) and afucosylated (3SGK) complexed with the Fc receptor subtype Fcγ RIIIA, and the Fc region of a murine immunoglobulin (1IGT). After few thousand steps of energy minimization on the resulting 3D mAb models, minimized final models were used to quantify interactions occurring between Fcγ RIIIA and the fucosylated/afucosylated Fc fragments. While fucosylation does not affect Fab-TNF α interactions, we found that in the absence of fucosylation the Fc-mAb domain and Fcγ RIIIA are closer and new strong interactions are established between G129 of the receptor and S301 of the Chimera 2 Fc mAb; new polar interactions are also established between the Chimera 2 Fc residues Y299, N300, and S301 and the Fcγ RIIIA residues K128, G129, R130, and R155. These data help to explain the reduced ADCC observed in the fucosylated mAbs suggesting the specific AA residues involved in binding interactions.

Identification of new highly selective inhibitors of the human ADP/ATP carriers by molecular docking and in vitro transport assays.

Mitochondrial carriers are proteins that shuttle a variety of metabolites, nucleotides and coenzymes across the inner mitochondrial membrane. The mitochondrial ADP/ATP carriers (AACs) specifically translocate the ATP synthesized within mitochondria to the cytosol in exchange for the cytosolic ADP, playing a key role in energy production, in promoting cell viability and regulating mitochondrial permeability transition pore opening. In Homo sapiens four genes code for AACs with different tissue distribution and expression patterns. Since AACs are dysregulated in several cancer types, the employment of known and new AAC inhibitors might be crucial for inducing mitochondrial-mediated apoptosis in cancer cells. Albeit carboxyatractyloside (CATR) and bongkrekic acid (BKA) are known to be powerful and highly selective AAC inhibitors, able to induce mitochondrial dysfunction at molecular level and poisoning at physiological level, we estimated here for the first time their affinity for the human recombinant AAC2 by in vitro transport assays. We found that the inhibition constants of CATR and BKA are 4 nM and 2.0 µM, respectively. For finding new AAC inhibitors we also performed a docking-based virtual screening of an in-house developed chemical library and we identified about 100 ligands showing high affinity for the AAC2 binding region. By testing 13 commercially available molecules, out of the 100 predicted candidates, we found that 2 of them, namely suramin and chebulinic acid, are competitive AAC2 inhibitors with inhibition constants 0.3 µM and 2.1 µM, respectively. We also demonstrated that chebulinic acid and suramin are "highly selective" AAC2 inhibitors, since they poorly inhibit other human mitochondrial carriers (namely ORC1, APC1 and AGC1).

Intravascular ultrasound based dose assessment in endovascular brachytherapy.

BACKGROUND: the role of endovascular brachytherapy in restenosis prevention is well documented. Dose is usually prescribed at a fixed distance from the source axis by angiographic quantification of vessel diameter. Recently, intravascular ultrasound (IVUS) was introduced in dose prescription, allowing a better evaluation of the vessel anatomy. This study retrospectively explores the difference between prescription following angiographic vessel sizing and delivered dose calculated with IVUS. METHODS AND RESULTS: Seventeen lesions were studied with IVUS, identifying on irradiated segment, three sections on which measuring minimal and maximal distance from the centre of IVUS catheter to the adventitia; using dedicated software, corresponding doses were calculated. The dose ranged widely, with maximal and minimal values of 71.6 and 4.9 Gy; furthermore, heterogeneity in dose among different sections was observed. In the central section, the maximal dose was 206% of the one prescribed with the QCA model at 2 mm from the source axis, while the minimal dose was 96%. In proximal and distal sections, respective values were 182, 45, 243, and 122%. CONCLUSIONS: Our analysis confirmed the dose inhomogeneity delivered with an angiographic fixed-dose prescription strategy. A dose variation was found along the irradiated segment due to the differences in vessel thickness. IVUS emerged as an important tool in endovascular brachytherapy, especially for irregular-shaped vessels.

A case of gastric adenocarcinoma associated with giant-cell phlebitis.

A 60-year-old male patient with advanced gastric adenocarcinoma was treated by subtotal gastrectomy with dissection of the regional lymph nodes. Microscopic examination of the tumour revealed tubular adenocarcinoma which invaded the muscularis propria. There was no evidence of metastatic carcinoma in the dissected lymph nodes (pT2N0Mx). Granulomatous reaction comprising epithelioid cells and giant cells involved subserosal muscular veins, adjacent to the carcinoma tissue. Fibrinoid necrosis, with or without infiltration of eosinophils, was noted within the lumen of some veins. The acid-fast and fungal stains were negative. Remnants of parasites were not identified in serial sections of the paraffin blocks. No pulmonary disease was evident on radiographic or pulmonary examination. The presence of granulomatous destruction of muscular veins with sparing of arteries suggested the diagnosis of giant-cell phlebitis. To our knowledge, there have been no previous reports regarding an association between giant-cell phlebitis and advanced gastric adenocarcinoma.

[Voluntary or accidental ingestion of foreign bodies: clinical considerations in 142 cases]. / L'ingestione volontaria o accidentale di corpi estranei: considerazioni cliniche su 142 casi.

The authors report on a series of 142 patients who had swallowed foreign bodies over the period 1981-1999. After outlining the various ways in which the foreign bodies were swallowed and the fact that they were eliminated spontaneously by natural routes in 80-90% of cases, the authors deal at some length with the serious complications that occurred in some of these cases, which, as a result of their characteristics and mode of ingestion, may require emergency surgery for their resolution. In particular, the authors describe 6 cases of foreign bodies that were urgently removed by endoscopy and also describe 3 cases in detail (1 perforation and 2 bowel obstructions) in which a laparotomy was required not only to correct the complication but also to definitively clarify the diagnosis.

Riboflavin responsive mitochondrial myopathy is a new phenotype of dihydrolipoamide dehydrogenase deficiency. The chaperon-like effect of vitamin B2.

Dihydrolipoamide dehydrogenase (DLD, E3) is a flavoprotein common to pyruvate, α-ketoglutarate and branched-chain α-keto acid dehydrogenases. We found two novel DLD mutations (p.I40Lfs*4; p.G461E) in a 19 year-old patient with lactic acidosis and a complex amino- and organic aciduria consistent with DLD deficiency, manifesting progressive exertional fatigue. Muscle biopsy showed mitochondrial proliferation and lack of DLD cross-reacting material. Riboflavin supplementation determined the complete resolution of exercise intolerance with the partial restoration of the DLD protein and disappearance of mitochondrial proliferation in the muscle. Morphological and functional studies support the riboflavin chaperon-like role in stabilizing DLD protein with rescue of its expression in the muscle.