To accelerate the Zika beat: Candidate design for RNA interference-based therapy.

Zika virus infection is associated with the development of severe neurological disorders in adults and newborns. Although at the moment Zika virus outbreak is not threatening to become again an emergency, infection cases are still being sporadically reported and there is still no effective therapy available. A possible treatment to suppress Zika replication is represented by short interfering RNAs (siRNAs), since they have been successfully used even against Ebola, H5N1 and SARS viruses and clinical trials of siRNA-based drugs are ongoing. In order to speed up the time consuming experimental validation of effective siRNAs, we have performed a comprehensive bioinformatic analysis to design only a few promising siRNAs against Zika virus. Besides siRNA efficacy, we paid attention to broad-spectrum antiviral activity, obtained by analysing all known Zika genomes, and siRNA safety, by excluding siRNAs that could potentially provoke an immune response or interfere with host mRNAs, lncRNAs, circRNAs and RNA binding proteins. In Zika genome we identified several highly conserved regions targetable by only 20 siRNAs. In particular, only a few siRNAs survived highly stringent criteria for siRNA safety. Notably, two of our candidate siRNAs have been successfully used against other flaviviruses like Zika, both in in vitro and in vivo models. Since they were effective against two different flaviviruses, by targeting a highly conserved region, it is reasonable to hypothesize that they could be active also against Zika. Therefore, we encourage researchers to experimentally validate these promising siRNAs.

Identification of candidate miRNA biomarkers for pancreatic ductal adenocarcinoma by weighted gene co-expression network analysis.

PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a dismal prognosis which is, among others, due to a lack of suitable biomarkers and therapeutic targets. Previously, basic gene expression analysis methods have been used for their identification, but recently new algorithms have been developed allowing more comprehensive data analyses. Among them, weighted gene co-expression network analysis (WGCNA) has already been applied to several cancer types with promising results. METHODS: We applied WGCNA to miRNA expression data from PDAC patients. Specifically, we processed microarray-based expression data of 2555 miRNAs in serum from 100 PDAC patients and 150 healthy subjects. We identified network modules of co-expressed miRNAs in the healthy subject dataset and verified their preservation in the PDAC dataset. In the non-preserved modules, we selected key miRNAs and carried out functional enrichment analyses of their experimentally known target genes. Finally, we tested their prognostic significance using overall survival analyses. RESULTS: Through WGCNA we identified several miRNAs that discriminate healthy subjects from PDAC patients and that, therefore, may play critical roles in PDAC development. At a functional level, we found that they regulate p53, FoxO and ErbB associated cellular signalling pathways, as well as cell cycle progression and various genes known to be involved in PDAC development. Some miRNAs were also found to serve as novel prognostic biomarkers, whereas others have previously already been proposed as such, thereby validating the WGCNA approach. In addition, we found that these novel data may explain at least some of our previous PDAC gene expression analysis results. CONCLUSIONS: We identified several miRNAs critical for PDAC development using WGCNA. These miRNAs may serve as biomarkers for PDAC diagnosis/prognosis and patient stratification, and as putative novel therapeutic targets.

The choice of endogenous controls in exosomal microRNA assessments from biofluids.

The assessment of differentially expressed microRNAs in patients and healthy controls is important to identify potential tumor biomarkers. Recently, it has been shown that the microRNA levels in exosomes are more correlated with the clinical-pathological variables than vesicle-free microRNAs (miRNAs) in biofluids; therefore, there is an increasing interest in these specific evaluations. However, these measurements can be affected by experimental problems that not always are evaluated and/or by inadequate procedural choices. In particular, exosome isolation and miRNA extraction procedures are crucial to avoid contaminations, and even the choice of the most suitable purity controls is important. Moreover, a stable endogenous RNA should be used for normalization of miRNA expression obtained by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) in order to make these measures comparable among different samples. A rushed choice of the endogenous control can bias study conclusions without revealing inconsistencies. Unfortunately, a few studies systematically identified the best normalizer for their specific experimental context. Instead, sometimes, the normalization procedures were performed in a disputable way or the normalizer choices simply based on the previous literature. Here, we reviewed the studies where the exosomal miRNA profiling was assessed in human biofluids to point out the adopted procedures and the specific endogenous controls chosen for normalization.

In vitro H2O2 stress and patterns of mitochondrial damage in the NCTC 2544 continuous cell line--a morphologic and morphometric study.

The morpho-functional and energy condition of NCTC 2544 cells exposed for 1 hr to a high concentration of H2O2 (500 microM) was studied at 4 and 24 hr to investigate the short- and medium-term biomolecular mechanisms affecting energetic mitochondrial capability. Morphometric data obtained from ultrastructural investigations clearly showed significant modifications of the different mitochondrial parameters--numerical density (Nv), volume density (Vv) and Vv/Nv ratio, in interkinetic, apoptotic and mitotic cells after H2O2 exposure (from 4 to 24 hr). These results were confirmed by the detection at 24 hr of mitochondrial cytochrome c release in the cytosol, indicating impairment in mitochondrial membrane permeability. Data supporting these observations were obtained from the MTT test which showed reduced cell viability in H2O2 treated cultures at 4 hr and an even greater decrement at 24 hr. In conclusion our data imply that significant cause-effect relationships exist between the toxicity of reactive oxygen species (i.e. 500 microM H2O2) and morpho-structural mitochondrial damage in interkinetic, apoptotic and mitotic cells, respectively. They support previous results present both in the literature and also in one of our earlier papers which show that early nuclear DNA damage could initiate mitochondrial or intrinsic apoptotic pathway after H2O2 exposure.

Chiral HPLC separation and CD spectra of the enantiomers of the alkaloid tacamonine and related compounds.

The HPLC enantiomeric separation of racemic indole alkaloids tacamonine, 17 alpha-hydroxytacamonine, deethyleburnamonine, and vindeburnol was accomplished using Chiralpak AD and Chiralcel OD as chiral stationary phases. Small structural differences affect the enantioselectivity ability of these phases. Single enantiomers of tacamonine and vindeburnol were isolated by semipreparative HPLC and their CD spectra and optical rotations were measured.

Total antioxidant capacity and nuclear DNA damage in keratinocytes after exposure to H2O2.

Studies of oxidative stress have classically been performed by analyzing specific, single antioxidants. In this study, susceptibility to oxidative stress in the human keratinocyte cell line NCTC2544 exposed to hydrogen peroxide (H2O2) was measured by the TOSC (total oxyradical scavenging capacity) assay, which discriminates between the antioxidant capacity toward peroxyl radicals and hydroxyl radical. The generation of H2O2-induced DNA damage, total antioxidant capacity and levels of antioxidant enzymes (catalase, superoxide dismutase, glutathione reductase, glutathione S-transferase, glutathione peroxidase) were studied. Exposure to H2O2-induced DNA damage that was gradually restored while a significant reduction in cellular TOSC values was obtained independently of stressor concentrations and the degree of DNA repair. Whereas TOSC values and cell resistance to H2O2 showed a good relationship, the extent of DNA damage is independent from cellular total antioxidant capacity. Indeed, maximum DNA damage and cell mortality were observed in the first 4 h, whereas TOSC remained persistently low until 48 h. Catalase levels were significantly lower in exposed cells after 24 and 48 h. Keratinocytes exposed after 48 h to a second H2O2 treatment exhibited massive cell death. A possible linkage was observed between TOSC values and NCTC2544 resistance to H2O2 challenge. The TOSC assay appears to be a useful tool for evaluating cellular resistance to oxidative stress.

Separation of the four pairs of enantiomers of vincamine alkaloids by enantioselective high-performance liquid chromatography.

The four enantiomeric pairs of vincamine group alkaloids were separated by HPLC using Chiralpak AD as chiral stationary phase (CSP) and various n-hexane-2-propanol and n-hexane-ethanol mobile phases. (+)-cis-Vincamine, which is used in pharmaceutical preparations, is eluted much faster than its optical isomer, with separation factors of 2.4 and 3.5, respectively in these mobile phases. Other CSPs gave negative results. A chiral recognition mechanism is proposed and circular dichroism spectra of the individual enantiomers are presented.

Biochemical changes in transplanted rat liver stored in University of Wisconsin and Euro-Collins solutions.

BACKGROUND: Liver ischemia/reperfusion injury is a severe problem in transplantation, and preservation solutions could be critical for liver viability. The aim of our study was to evaluate the cytosolic and mitochondrial glutathione levels, the glyoxalase II activity, and the mitochondrial hydroperoxide contents of livers stored in different preservation solutions for 7 or 24 h and after transplantation. MATERIALS AND METHODS: Orthotopic liver transplantation was performed without reconstruction of the hepatic artery. The livers were stored at 4 degrees C for 7 or 24 h in University of Wisconsin or Euro-Collins solutions. Portions of livers before and after transplantation were homogenized and mitochondria isolated. RESULTS: Cytosolic glutathione levels were decreased in all stored livers and after transplantation. In livers stored with University of Wisconsin solution, mitochondrial glutathione was unchanged during cold storage and no significant decrease has been found after reperfusion, whereas in livers stored in Euro-Collins solution, mitochondrial glutathione was decreased and a further significant decrease was found 30 min after reperfusion. Mitochondrial hydroperoxides were higher in livers stored in Euro-Collins solution than in University of Wisconsin solution after 30 min of reperfusion. Mitochondrial glyoxalase II did not show any change by reperfusion. CONCLUSION: We have demonstrated that rat liver stored in Euro-Collins solution suffered a severe depletion of mitochondrial GSH and a concomitant increase of hydroperoxides. The data obtained suggested that the livers stored with University of Wisconsin solution were probably less prone to ischemia/reperfusion injury after liver transplantation.

Specific interaction of cytosolic and mitochondrial glyoxalase II with acidic phospholipids in form of liposomes results in the inhibition of the cytosolic enzyme only.

Kinetics of cytosolic recombinant human glyoxalase II and bovine liver mitochondrial glyoxalase II were studied in the presence of liposomes made of different phospholipids (PLs). Neutral PLs such as egg phosphatidylcholine or dipalmitoylphosphatidylcholine did not affect the enzymatic activity of either enzymatic form. Liposomes made of dioleoyl phosphatidic acid or cardiolipin or phosphatidylserine also did not affect the enzymatic activity of mitochondrial glyoxalase II. Conversely, these negatively charged PLs exerted noncompetitive inhibition on cytosolic glyoxalase II only, dioleoyl phosphatidic acid and bovine brain phosphatidylserine exerting the highest and lowest inhibition, respectively. Binding studies, carried out by using a resonant mirror biosensor, revealed that liposomes made of negatively charged PLs interact specifically with both enzymatic forms of glyoxalase II, whereas interactions were not detected with neutral PLs. Once bound on glyoxalase II, negatively charged liposomes could not be removed by 3 M NaCl, suggesting that interactions between glyoxalase II and negatively charged PLs, besides ionic, may be also hydrophobic. These data suggest a possible role of negatively charged phospholipids in the regulation of level of lactoylglutathione in the cell. The data are also discussed in terms of a possible regulation of reduced glutathione supply to mitochondria.

Mitochondrial contribution to metabolic changes in the digestive gland of Mytilus galloprovincialis during anaerobiosis.

The activities of several enzymes and the levels of metabolites have been measured in the digestive gland of Mytilus galloprovincialis exposed to increasing hypoxia from 7 to 168 hr. A sharp decrease of pyruvate kinase was observed after 7 hr. The anoxic enzyme showed increased Km for phosphoenolpyruvate and decreased apparent Ki for alanine. Glyoxalase I was constant after up to 72 hr of exposure and then decreased. Phosphoenolpyruvate carboxykinase and alanopine dehydrogenase decreased. The metabolites alanine and succinate increased with hypoxia time, whereas D- and L-lactic and aspartic acids were undetectable and constant respectively. Mitochondrial formation of pyruvate from D-lactate was demonstrated in intact mitochondria isolated from the digestive gland of Mytilus galloprovincialis. The significance of the observed enzyme and metabolite changes in hypoxia is discussed in comparison with other invertebrate organisms. The role of mitochondria in the overall adaptive strategy of Mytilus galloprovincialis is discussed. J. Exp. Zool. 286:107-113, 2000.

Glutathione and ultrastructural changes in inflow occlusion of rat liver.

BACKGROUND: Liver ischemia/reperfusion is frequently associated with organ injury to which reactive oxygen species contribute. The aim of our study was to evaluate cytosolic and mitochondrial glutathione levels and morphological changes in hepatocytes of rat liver in an experimental model of ischemia/reperfusion. MATERIALS AND METHODS: The experimental procedure consisted of temporary interruption of blood flow to the left lateral and medial hepatic lobes for different lengths of time and, in some cases, subsequent reperfusion. Cytosolic and mitochondrial glutathione levels were evaluated and ultrastructural analysis was carried out for all samples. RESULTS: Ischemic lobes showed ultrastructural changes in relationship with the increase in ischemia time. Total glutathione levels did not show variations in ischemic lobes and sham lobes with respect to control rats during ischemia only. Instead, during reperfusion, significant ultrastructural alterations of the hepatocytes and a significant depletion of glutatione in cytosolic and mitochondrial compartments were evident. The sham lobes also showed a significant glutathione decrement. Increased oxidized glutathione (GSSG) levels were found during ischemia both in ischemic lobes and in sham lobes. During reperfusion GSSG was found to a minor extent, in the cytosolic compartment. In mitochondria GSSG levels were also high during reperfusion. CONCLUSIONS: We conclude that depletion of glutathione contributes to impaired liver after reperfusion following ischemia but depletion of glutathione alone does not induce changes in the morphology of the hepatocytes. Glutathione depletion and a greater quantity of GSSG, even in sham lobes, may indicate a metabolic alteration which spreads to compartments that are not involved in ischemia/reperfusion.

[Bio-metabolic changes produced by 2 commercial fluoride-containing compounds on human keratinocytes]. / Alterazioni bio-metaboliche indotte da due composti fluorati commerciali su cheratinociti umani.

BACKGROUND: Although fluoride has been used for decades either systemically or topically to prevent dental caries, the cellular and molecular mechanisms underlying its action are poorly understood. METHODS: An in vitro study of the human keratinocyte cell line NCTC 2544 was conducted in the presence of two different fluoride-containing commercial compounds (Zymafluor and Elmex) to investigate their toxicity threshold and the sequence of events involved in fluoride ion toxicity in this cell population. The toxicity threshold was determined by incubating cells with rising concentrations of Zymafluor and Elmex for 20 h. The study of the sequence of events involved in ion toxicity was performed through a time-effect study by exposing cells to 4 mM fluoride ions and testing them at 2, 6, and 20 h. Cell viability and ultrastructural parameters were assessed: degree of confluence, semiquantitative assessment of dead cells and debris in the supernatant, and morphology. RESULTS: Ultrastructural morphological analysis showed different cell behaviours with the two compounds; moreover, their toxic effect appeared to be both concentration- and time-dependent. CONCLUSIONS: These data underline the susceptibility of the intracellular communication system to fluoride and show that exceeding the therapeutic dose of fluoride involves substantial risk of toxicity.

Effect of methylglyoxal on Bufo bufo embryo development: morphological and biochemical aspects.

Methylglyoxal (2-oxopropanal) is a cytotoxic compound that can be formed endogenously as a by-product of glycolytic pathway; so its concentration is expected to increase when glycolysis activity increases such as during embryo development. In this work we study the effect of exogenous methylglyoxal on development and embryo viability during Bufo Bufo development and on the enzymes and cofactors involved in its detoxication process (glyoxalase I and II, reduced glutathione and glyceraldehyde 3-phosphate dehydrogenase). The results show that exogenous methylglyoxal does not affect the enzymatic pattern until stage 20, while it induces a significant activity decrease of the tested enzymes at stage 25. On the contrary methylglyoxal positively influences the reduced glutathione concentration at all the considered stages. At morphological and histological levels methylglyoxal causes a strong retardation of cell division in the early stages, that results in various abnormalities in the late development. In conclusion, methylglyoxal enters the embryo and is antiproliferative and teratogenic: the data further supports the hypothesis of the importance of the glyoxalase system in the process of cell growth and division.

Studies on the life prolonging effect of food restriction: glutathione levels and glyoxalase enzymes in rat liver.

Cytosolic and mitochondrial levels of glutathione (GSH) as well as the activities of glyoxalase I (GI) and glyoxalase II (GII), GSH-dependent enzymes involved in the detoxification of 2-ketoaldehydes, were investigated in the liver of ad libitum (AL) fed and food restricted (FR) rat during aging. Both cytosolic and mitochondrial GSH level was lower in old than in adult AL fed rats. Food restriction did not prevent this decrease, but its extent was attenuated considering the cytosolic GSH. As regards the mitochondrial GSH, its content was higher in adult FR animals than in the age-matched AL fed ones. Thus, the subsequent age-dependent decrease of GSH, occurring also in FR animals, resulted in a thiol concentration not different from that observed in young and adult AL fed animals. Considering the enzymatic activities, cytosolic GI decreased in old rats irrespective of diet, whereas GII activity remained constant in all the experimental groups. The higher glutathione content found in both cellular compartments of old FR rats as compared to the old AL fed ones, could help to explain the life prolonging effect of FR treatment. Moreover, the observation that the activity of glyoxalases was not influenced by food restriction does not necessarily mean that the cells of diet-conditioned animals are scarcely protected against the toxic effect of methylglyoxal. Indeed, the production of this compound should be lower in FR animals as compared to AL fed ones, due to the lower level serum glucose concentration during the life span of the former with respect to the latter group.

Structural characterization of human glyoxalase II as probed by limited proteolysis.

Human glyoxalase II is partially proteolyzed by trypsin, under non denaturing conditions, only at the level of the C-terminal region. The proteolytic cleavage resulted in an inactivation of the enzyme without loss of the secondary structure. Sodium dodecyl sulphate polyacrylamide gel-electrophoresis and microsequence analysis showed that the glyoxalase II is proteolyzed at the level of Arg 184 and Lys 230 and undergoes a third cleavage in a region located at the beginning of the supposed C-terminal domain. The proteolysis occurs either in the presence or in the absence of specific inhibitors. Our limited proteolysis experiments and secondary structure prediction give evidence for the presence of two domains characterized by different pattern of secondary structure.

Dietary restriction affects antioxidant levels in rat liver mitochondria during ageing.

Six experimental groups of young (7-month-old) and aged (24-32-month-old) rats, underwent different dietary manipulations (i.e. dietary restriction and/or a vitamin E-depleted diet), and their liver mitochondria were assayed for several antioxidants and peroxidation markers. Glutathione levels were affected both by age and dietary treatment. Coenzyme Q9 and C0Q10 showed the highest levels in the oldest rats where ageing, as well as other oxidative stresses, could induce ubiquinone biosynthesis.

Glyoxalase II and glutathione levels in rat liver mitochondria during cold storage in Euro-Collins and University of Wisconsin solutions.

Glutathione and glyoxalase II levels were evaluated in cytosolic and mitochondrial compartments of rat liver after 7 and 24 hr of cold storage in University of Wisconsin (UW) and Euro-Collins solutions. 1-4 A similar time-dependent depletion of cytosolic glutathione up to about 60% of control values was observed in both Euro-Collins and UW solutions. Cytosolic glyoxalase II showed activity oscillations in livers stored in Euro-Collins but not in UW. Mitochondrial glutathione and glyoxalase II were severely depleted soon after 7 hr of cold storage in Euro-Collins, whereas the same parameters did not change in liver stored in UW after 24 hr. UW is confirmed to be the most suitable solution for liver cold storage and we conclude that mitochondrial glutathione and glyoxalase II can be important parameters in assessing mitochondrial and cell function.

Molecular cloning, heterologous expression, and characterization of human glyoxalase II.

A clone encoding glyoxalase II has been isolated from a human adult liver cDNA library. The sequence of 1011 base pairs consists of a full-length coding region of 780 base pairs, corresponding to a protein with a calculated molecular mass of 28,861 daltons. Identities (50-60%) were found to partial 5' and 3' cDNA sequences from Arabidopsis thaliana as well as within a limited region of glutathione transferase I cDNA from corn. A vector was constructed for heterologous expression of glyoxalase II in Escherichia coli. For optimal yield of enzyme, silent random mutations were introduced in the 5' coding region of the cDNA. A yield of 25 mg of glyoxalase II per liter of culture medium was obtained after affinity purification with immobilized glutathione. The recombinant enzyme had full catalytic activity and kinetic parameters indistinguishable from those of the native enzyme purified from human erythrocytes.

Fluorenone 1,4-dihydropyridine derivatives with cardiodepressant activity: enantiomeric separation by chiral HPLC and conformational aspects.

The direct HPLC enantiomeric separation of five fluorenone-1,4-dihydropyridine-3,5-dicarboxylic diesters has been achieved using a Chiralpak AD stationary phase obtaining simultaneously good enantioselectivities, resolution factors, and elution times. CD spectra of the individual enantiomers for two compounds were measured. Thermodynamic parameters associated with the adsorption equilibria of the enantiomers with the chiral stationary phase were obtained from HLPC runs at various temperatures. The conformational preferences of the synperiplanar fluorenone group and of the cis/cis ester groups were obtained by 1H NMR spectra, including NOE experiments.

Direct high-performance liquid chromatographic separation of the enantiomers of methoxy and hydroxy derivatives of 3,4-dihydro-3-(dipropylamino)-2H-1-benzopyrans with dopaminergic activity.

The direct HPLC resolution of the enantiomers of methoxy and hydroxy derivatives of 3,4-dihydro-3-(dipropylamino)-2H-1-benzopyrans and of unsubstituted amino compounds was achieved using Chiralcel OD and/or Chiralpak AD stationary phases. The position of the substituent (methoxyl or hydroxyl) in the aromatic ring has a strong effect on the enantioselectivity. Circular dichroism spectra of the single enantiomers of one compound were measured.