Alignment of high resolution mass spectra: development of a heuristic approach for metabolomics

One of the challenges of using mass spectrometry for metabolomic analyses of samples consisting of thousands of compounds is that of peak identification and alignment. This paper addresses the issue of aligning mass spectral data from different samples in order to determine average component m/z peak values. The alignment scheme developed takes the instrument m/z measurement error into consideration in order to heuristically align two or more samples using a technique comparable to automated visual inspection and alignment. The results obtained using mass spectral profiles of replicate human urine samples suggest that this heuristic alignment approach is more efficient than other approaches using hierarchical clustering algorithms. The output consists of an average m/z and intensity value for the spectral components together with the number of matches from the different samples. One of the major advantages of using this alignment strategy is that it eliminates the boundary problem that occurs when using predetermined fixed bins to identify and combine peaks for averaging and the efficient runtime allows large datasets to be processed quickly.     

The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink

Nitrous oxide (N₂O) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to nitrogen gas (N₂) by bacteria and archaea harboring the N₂O reductase (N₂OR), which is the only known N₂O sink in the biosphere. Despite its crucial role in mitigating N₂O emissions, knowledge of the N₂OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N₂OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N₂O-reducing communities. Examination of N₂OR structural elements not considered in the phylogeny revealed that the two clades differ in their signal peptides, indicating differences in the translocation pathway of the N₂OR across the membrane. Sequencing of environmental clones of the previously undetected nosZ lineage in various environments showed that it is widespread and diverse. Using quantitative PCR, we demonstrate that this clade was most often at least as abundant as the other, thereby more than doubling the known extent of the overall N₂O-reducing community in the environment. Furthermore, we observed that the relative abundance of nosZ from either clade varied among habitat types and environmental conditions. Our results indicate a physiological dichotomy in the diversity of N₂O-reducing microorganisms, which might be of importance for understanding the relationship between the diversity of N₂O-reducing microorganisms and N₂O reduction in different ecosystems.     

Malate-aspartate shuttle enzymes in rat brain regions, liver and heart during alloxan diabetes and insulin replacement

Regionally selective and time-dependent variations were observed in the activity of brain aspartate aminotransferase at early phases of diabetes. Malate dehydrogenase activity showed an opposite pattern of changes in soluble and particulate fractions of cerebral hemispheres and brain stem, with cerebellum showing consistent increase in the activity. The activity of both the enzymes increased significantly in liver, in contrast to heart where malate dehydrogenase activity decreased in particulate fraction. Insulin treatment to diabetic animals restored the enzymes to near control levels at early stages of diabetes, except in liver. The results indicate that malate-aspartate shuttle is probably stimulated under diabetic conditions to enable glycolysis to continue and ATP levels to be restored partially, particularly in cerebellum and liver.     

A mutant of Escherichia coli which accumulates large amounts of coproporphyrin

A mutant of Escherichia coli which accumulates a large amount of coproporphyrin, presumably because of a block in heme biosynthesis, has been isolated after nitrosogunidine mutagenesis. On rich media, the mutant forms colonies which give bright orange fluorescence when illuminated with ultraviolet light. The mutant appears to be similar to a Salmonella typhimurium mutant, deficient in uroporphyrinogen III cosynthase, described by Sasarman and Desrochers ((1976) J. Bacteriol. 128, 717–721). A striking property of the mutant is that coproporphyrin is retained within the cells in rich media but is almost totally excreted out of cells in minimal glucose medium.     

Changes in Monoamine Oxidase Activity in Rat Brain During Alloxan Diabetes

Abstract: The effect of alloxan diabetes on the activity of monoamine oxidase was studied in three regions of the rat brain at various time intervals after the onset of diabetes. It was observed that monoamine oxidase activity was decreased at early time intervals after diabetes, followed by a recovery in all three regions of the brain. A reversal of the effect was observed with insulin administration to the diabetic rats.