Meta-analysis of untargeted metabolomic data from multiple profiling experiments

metaXCMS is a software program for the analysis of liquid chromatography/mass spectrometry-based untargeted metabolomic data. It is designed to identify the differences between metabolic profiles across multiple sample groups (e.g., 'healthy' versus 'active disease' versus 'inactive disease'). Although performing pairwise comparisons alone can provide physiologically relevant data, these experiments often result in hundreds of differences, and comparison with additional biologically meaningful sample groups can allow for substantial data reduction. By performing second-order (meta-) analysis, metaXCMS facilitates the prioritization of interesting metabolite features from large untargeted metabolomic data sets before the rate-limiting step of structural identification. Here we provide a detailed step-by-step protocol for going from raw mass spectrometry data to metaXCMS results, visualized as Venn diagrams and exported Microsoft Excel spreadsheets. There is no upper limit to the number of sample groups or individual samples that can be compared with the software, and data from most commercial mass spectrometers are supported. The speed of the analysis depends on computational resources and data volume, but will generally be less than 1 d for most users. metaXCMS is freely available at http://metlin.scripps.edu/metaxcms/.     

Complete genome sequencing of a novel newcastle disease virus isolate circulating in layer chickens in the dominican republic

Newcastle disease virus (NDV) was isolated from an outbreak in layer chickens in the Dominican Republic in 2008. Infections with this isolate led to a 100% apparent case fatality rate in birds. Complete genome sequencing revealed that the isolate does not belong to any of the previously described NDV genotypes. Similarly, large differences were observed in the amino acid sequence of the fusion and hemagglutinin-neuraminidase proteins in comparison with all known NDV genotypes, suggesting the existence of an unknown reservoir for NDV. The work presented here represents the first complete genome sequence of NDV in the Dominican Republic.     

Reactive oxygen species are involved in ferroportin degradation induced by ceruloplasmin mutant Arg701Trp

The ceruloplasmin mutant R701W, that causes a dramatic phenotype in the young heterozygous patient carrying this mutation, has been shown to have profound effects also in cell culture models. Here we show that Golgi rearrangement and degradation of the iron exporter ferroportin, that follow transfection of cells with this mutant, are accompanied by the massive production of reactive oxygen species (ROS) in the cell. Scavenging ROS production with different antioxidants, including reduced glutathione and zinc, restores Golgi morphology and rescues ferroportin on the cell membrane.     

Design,synthesis and evaluation of a novel double pro-drug: INX-08189. A new clinical candidate for hepatitis C virus

We herein report a novel double pro-drug approach applied to the anti-HCV agent 2′-β-C-methyl guanosine. A phosphoramidate ProTide motif and a 6-O-methoxy base pro-drug moiety are combined to generate lipophilic prodrugs of the monophosphate of the guanine nucleoside. Modification of the ester and amino acid moieties lead to a compound INX-08189 that exhibits 10 nM potency in the HCV genotype 1b subgenomic replicon, thus being 500 times more potent than the parent nucleoside. The potency of the lead compound INX-08189 was shown to be consistent with intracellular 2′-C-methyl guanosine triphosphate levels in primary human hepatocytes. The separated diastereomers of INX-08189 were shown to have similar activity in the replicon assay and were also shown to be similar substrates for enzyme processing. INX-08189 has completed investigational new drug enabling studies and has been progressed into human clinical trials for the treatment of chronic HCV infection.     

Design,synthesis and evaluation of (E)-α-benzylthio chalcones as novel inhibitors of BCR-ABL kinase

Novel (E)-α-benzylthio chalcones are reported with preliminary in vitro activity data indicating that several of them are potent inhibitors (comparable to imatinib, the reference compound) of BCR-ABL phosphorylation in leukemic K562 cells, known to express high levels of BCR-ABL. The ability of such compounds to significantly inhibit K562 cell proliferation suggests that this scaffold could be a promising lead for the development of anticancer agents that are able to block BCR-ABL phosphorylation in leukemic cells.     

Nutritional Requirements of Methanosarcina sp. Strain TM-1

Methanosarcina sp. strain TM-1, an acetotrophic, thermophilic methanogen isolated from an anaerobic sludge digestor, was originally reported to require an anaerobic sludge supernatant for growth. It was found that the sludge supernatant could be replaced with yeast extract (1 g/liter), 6 mM bicarbonate-30% CO₂, and trace metals, with a doubling time on methanol of 14 h. For growth on either methanol or acetate, yeast extract could be replaced with CaCl₂ · 2H₂O (13.6 μM minimum) and the vitamin p-aminobenzoic acid (PABA, ca. 3 nM minimum), with a doubling time on methanol of 8 to 9 h. Filter-sterilized folic acid at 0.3 μM could not replace PABA. The antimetabolite sulfanilamide (20 mM) inhibited growth of and methanogenesis by Methanosarcina sp. strain TM-1, and this inhibition was reversed by the addition of 0.3 μM PABA. When a defined medium buffered with 20 mM N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid was used, it was shown that Methanosarcina sp. strain TM-1 required 6 mM bicarbonate-30% CO₂ for optimal growth and methanogenesis from methanol. Cells growing on acetate were less dependent on bicarbonate-CO₂. When we used a defined medium in which the only organic compounds present were methanol or acetate, nitrilotriacetic acid (0.2 mM), and PABA, it was possible to limit batch cultures of Methanosarcina sp. strain TM-1 for nitrogen at NH₄⁺ concentrations at or below 2.0 mM, in marked contrast with Methanosarcina barkeri 227, which fixes dinitrogen when grown under NH₄⁺ limitation.     

Release-enhancing pre-synaptic muscarinic and nicotinic receptors co-exist and interact on dopaminergic nerve endings of rat nucleus accumbens

Dopaminergic nerve endings in the corpus striatum possess nicotinic (nAChRs) and muscarinic cholinergic receptors (mAChRs) mediating release of dopamine (DA). Whether nAChRs and mAChRs co-exist and interact on the same nerve endings is unknown. We here investigate on these possibilities using rat nucleus accumbens synaptosomes pre-labeled with [³H]DA and exposed in superfusion to cholinergic receptor ligands. The mixed nAChR–mAChR agonists acetylcholine (ACh) and carbachol provoked [³H]DA release partially sensitive to the mAChR antagonist atropine but totally blocked by the nAChR antagonist mecamylamine. Addition of the mAChR agonist oxotremorine at the minimally effective concentration of 30 μmol/L, together with 3, 10, or 100 μmol/L (−)nicotine provoked synergistic effect on [³H]DA overflow. The [³H]DA overflow elicited by 100 μmol/L (−)nicotine plus 30 μmol/L oxotremorine was reduced by atropine down to the release produced by (−)nicotine alone and it was abolished by mecamylamine. The ryanodine receptor blockers dantrolene or 8-bromo-cADP-ribose, but not the inositol 1,4,5-trisphosphate receptor blocker xestospongin C inhibited the (−)nicotine/oxotremorine evoked [³H]DA overflow similarly to atropine. This overflow was partly sensitive to 100 nmol/L methyllycaconitine which did not prevent the synergistic effect of (−)nicotine/oxotremorine. Similarly to (−)nicotine, the selective α4β2 nAChR agonist RJR2403 exhibited synergism when added together with oxotremorine. To conclude, in rat nucleus accumbens, α4β2 nAChRs exert a permissive role on the releasing function of reportedly M₅ mAChRs co-existing on the same dopaminergic nerve endings.     

Direct measurement of the energy expenditure of physical activity in preterm infants

The energy cost of physical activity (EEA) has been estimated toaccount for 5-17% of total energy expenditure (TEE) in neonates. To directly measure EEA, a force plate was developed and validated tomeasure work outputs ranging from 0.3 to 40 kcal · kg¹ · day¹.By use of this force plate plus indirect calorimetry, TEE and EEA weremeasured and correlated with five activity states in 24 infants withgestational age of 31.6 ± 0.5 (SE) wk and postnatal age of 24.8 ± 3.7 days. TEE and EEA were 69.2 ± 1.5 and 2.4 ± 0.2 kcal · kg¹ · day¹,respectively. EEA per state was 0.5 ± 0.0 (quiet sleep), 2.4 ± 0.2 (active sleep), 2.8 ± 0.4 (quiet awake), 7.5 ± 0.8 (active awake), and 15.1 ± 2.3 (crying)kcal · kg¹ · day¹.This provides the first direct measurement of the contribution ofphysical activity to TEE in preterm infants and will enable measurementof caloric expenditure from muscle activity in various diseaseconditions and development of nursing strategies to minimize unnecessary energy losses.