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Many groups within the broad field of nanoinformatics are already developing data repositories and analytical tools driven by their individual organizational goals. Integrating these data resources across disciplines and with non-nanotechnology resources can support multiple objectives by enabling the reuse of the same information. Integration can also serve as the impetus for novel scientific discoveries by providing the framework to support deeper data analyses. This article discusses current data integration practices in nanoinformatics and in comparable mature fields, and nanotechnology-specific challenges impacting data integration. Based on results from a nanoinformatics-community-wide survey, recommendations for achieving integration of existing operational nanotechnology resources are presented. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines. This paper is one of a series of articles by the Nanomaterial Data Curation Initiative that address data issues such as data curation workflows, data completeness and quality, curator responsibilities, and metadata.

Graphical abstract, Highlights • Dendritic cells (DC) treated with 1,25-dihydroxyvitamin D (1,25D) alone show a tolerogenic DC phenotype. • 1,25D-treated DC show altered oxidative phosphorylation and electron transport. • 1,25D-treated DC show altered glycolysis and TCA cycle metabolism. • TCA effects of 1,25D enhance fatty acid synthesis by DC. • Fatty acid synthesis appears to be essential for DC tolerogenic effects of 1,25D., The active form of vitamin D, 1,25-dihydroxyvitamin D (1,25D) is a potent regulator of immune function, promoting anti-inflammatory, tolerogenic T cell responses by modulating antigen presentation by dendritic cells (DC). Transcriptomic analyses indicate that DC responses to 1,25D involve changes in glycolysis, oxidative phosphorylation, electron transport and the TCA cycle. To determine the functional impact of 1,25D-mediated metabolic remodelling, human monocyte-derived DC were differentiated to immature (+vehicle, iDC), mature (+LPS, mDC), and immature tolerogenic DC (+1,25D, itolDC) and characterised for metabolic function. In contrast to mDC which showed no change in respiration, itolDC showed increased basal and ATP-linked respiration relative to iDC. Tracer metabolite analyses using 13C -labeled glucose showed increased lactate and TCA cycle metabolites. Analysis of lipophilic metabolites of 13C-glucose revealed significant incorporation of label in palmitate and palmitoleate, indicating that 1,25D promotes metabolic fatty acid synthesis in itolDC. Inhibition of fatty acid synthesis in itolDC altered itolDC morphology and suppressed expression of CD14 and IL-10 by these cells. These data indicate that the ability of 1,25D to induce tolerogenic DC involves metabolic remodelling leading to synthesis of fatty acids.

Biological pathways are abstract and functional visual representations of existing biological knowledge. By mapping high-throughput data on these representations, changes and patterns in biological systems on the genetic, metabolic and protein level are instantly assessable. Many public domain repositories exist for storing biological pathways, each applying its own conventions and storage format. A pathway-based content review of these repositories reveals that none of them are comprehensive. To address this issue, we apply a general workflow to create curated biological pathways, in which we combine three content sources: public domain databases, literature and experts. In this workflow all content of a particular biological pathway is manually retrieved from biological pathway databases and literature, after which this content is compared, combined and subsequently curated by experts. From the curated content, new biological pathways can be created for a pathway analysis tool of choice and distributed among its user base. We applied this procedure to construct high-quality curated biological pathways involved in human fatty acid metabolism.

The toxic potency of three industrially used hydroxylamines was studied in human blood cells in vitro. The parent compound hydroxylamine and the O-ethyl derivative gave very similar results. Both compounds induced a high degree of methemoglobin formation and glutathione depletion. Cytotoxicity was visible as Heinz body formation and hemolysis. High levels of lipid peroxidation occurred, in this respect O-ethyl hydroxylamine was more active than hydroxylamine. In contrast H2O2 induced lipid peroxidation was lowered after O-ethyl hydroxylamine or hydroxylamine treatment, this is explained by the ferrohemoglobin dependence of H2O2 induced radical species formation. Glutathione S-transferase (GST) and NADPH methemoglobin reductase (NADPH-HbR) activities were also impaired, probably as a result of the radical stress occurring. The riboflavin availability was decreased. Other enzyme activities glutathione reductase (GR), glucose 6-phosphate dehydrogenase (G6PDH), glucose phosphate isomerase and NADH methemoglobin reductase, were not or only slightly impaired by hydroxylamine or O-ethyl hydroxylamine treatment. A different scheme of reactivity was found for N,O-dimethyl hydroxylamine. This compound gave much less methemoglobin formation and no hemolysis or Heinz body formation at concentrations up to and including 7 mM. Lipid peroxidase induction was not detectable, but could be induced by subsequent H2O2 treatment. GST and NADPH-HbR activities and riboflavin availability were not decreased. On the other hand GR and G6PDH activities were inhibited. These results combined with literature data indicate the existence of two different routes of hematotoxicity induced by hydroxylamines. Hydroxylamine as well as O-alkylated derivatives primarily induce methemoglobin, a process involving radical formation. The radical stress occurring is probably responsible for most other effects. N-alkylated species like N,O-dimethyl hydroxylamine primarily lead to inhibition of the protective enzymes G6PDH and GR. Since these enzymes play a key role in the protection of erythrocytes against oxidative stress a risk of potentiation during mixed exposure does exist.

A model system for the detection of reactive metabolites, using glutathionedepletion after microsomal activation, has been described previously. We developed a battery of complementary test systems using rat liver microsomes for metabolism and aqueous glutathione solutions, human erythrocytes or hemolysate derived therefrom, as target. Reactive metabolite formation and the ability of metabolites to pass the erythrocyte membrane were tested using 3-hydroxyacetanilide (3-HAA) and cyclophosphamide (CP) as substrates. Neither unchanged 3-HAA nor CP depleted glutathione in erythrocytes or in aqueous reduced glutathione solutions (GSH solutions). Addition of fortified normal or liver microsomes from rats pretreated with phenobarbital (PB microsomes) induced a 3-HAA/CP concentration-dependent glutathione depletion in both systems. With PB microsomes, higher depletions were found. While unchanged 3-HAA did not deplete aqueous GSH solutions or glutathione in erythrocytes, a significant depletion in hemolysate was found. The results indicate that both CP and 3-HAA metabolites are able to pass through the erythrocyte membrane. While both substances can metabolically be activated by rat liver microsomes, only 3-HAA can be activated by soluble factors in erythrocytes. However, unchanged 3-HAA has no effect on GSH in erythrocytes. This might be caused by an inability of unchanged 3-HAA to enter the erythrocyte. More generally, an adequate combination of the test systems described can be used to detect (a) the reactivity of unchanged substances and their metabolites, and (b) the ability of unchanged substances and their reactive metabolites to pass through the erythrocyte membrane.

A new program for continuous simulation is described. The program is block oriented, simulating the function of an analogue computer. C structures containing pointers to the calculation of their input functions were used for the individual blocks. The actual calculation order was determined from a sorted event list. After calculation events were inserted at the appropriate place in this list again. This procedure allowed for a variable and independent stepsize for the main blocks and for the introduction of discrete events. With typical applications a speed increase of about 500% was attained.

The effects were studied of improved oxygen supply on the integrity and metabolic activity towards dimethylacetamide of the isolated perfused rat liver. Improvement of oxygen supply by increased medium oxygenation or addition of chemical oxygen carriers (perfluortributylamine) or erythrocytes led to increased bile secretion. Leakage of lactate dehydrogenase and aspartate aminotransferase could be prevented during a 1-hr perfusion when either chemical oxygen carriers or erythrocytes were added. Improved medium oxygenation alone was not sufficient to prevent high enzyme leakage during the second half of the perfusion period. Histological evaluation confirmed the conclusion that less damage occurred when erythrocytes or perfluortributylamine were added to the perfusion medium. The metabolic clearance of dimethylacetamide by the perfused rat liver was not significantly improved when erythrocytes were added to the medium. The results show that addition of perfluortributylamine, or erythrocytes at a level of 4 g haemoglobin/litre, is necessary to maintain liver integrity for at least 1 hr in the liver perfusion system used in this study.

Human blood samples were treated in vitro with iodoacetamide. At low concentrations - less than 1 mM - only a low fraction of the beta 93 cysteine in hemoglobin was alkylated, whereas the alkylating reaction with glutathione was extensive. At higher iodoacetamide concentrations the glutathione pool became exhausted leading to more than proportional increases in the alkylation of the sulfhydryl group in hemoglobin. When diethyl maleate was used as a glutathione depletor prior to incubation with iodoacetamide, low concentrations of iodoacetamide were sufficient to obtain high degrees of hemoglobin sulfhydryl alkylation. N-Ethylmaleimide could not be used as glutathione depletor because the reaction with glutathione appeared to be reversible. The lower reactivity of the thiol group in hemoglobin in comparison with that of glutathione was also found for the isolated biomolecules. The protection of hemoglobin by glutathione present in the human erythrocyte renders the measurement of hemoglobin alkylation less attractive for biological effect monitoring. The sensitivity of such methods is lowered, while the important relation between the alkylation of hemoglobin and that of DNA in the target tissues is affected by interindividual differences in the ratios of the effectiveness of glutathione protection between erythrocytes and target cells.