Molecular Formula and METLIN Personal Metabolite Database Matching Applied to the Identification of Compounds Generated by LC/TOF-MS

In an effort to simplify and streamline compound identification from metabolomics data generated by liquid chromatography time-of-flight mass spectrometry, we have created software for constructing Personalized Metabolite Databases with content from over 15,000 compounds pulled from the public METLIN database (http://metlin.scripps.edu/). Moreover, we have added extra functionalities to the database that (a) permit the addition of user-defined retention times as an orthogonal searchable parameter to complement accurate mass data; and (b) allow interfacing to separate software, a Molecular Formula Generator (MFG), that facilitates reliable interpretation of any database matches from the accurate mass spectral data. To test the utility of this identification strategy, we added retention times to a subset of masses in this database, representing a mixture of 78 synthetic urine standards. The synthetic mixture was analyzed and screened against this METLIN urine database, resulting in 46 accurate mass and retention time matches. Human urine samples were subsequently analyzed under the same analytical conditions and screened against this database. A total of 1387 ions were detected in human urine; 16 of these ions matched both accurate mass and retention time parameters for the 78 urine standards in the database. Another 374 had only an accurate mass match to the database, with 163 of those masses also having the highest MFG score. Furthermore, MFG calculated a formula for a further 849 ions that had no match to the database. Taken together, these results suggest that the METLIN Personal Metabolite database and MFG software offer a robust strategy for confirming the formula of database matches. In the event of no database match, it also suggests possible formulas that may be helpful in interpreting the experimental results.     

Mutation load in melanoma is affected by MC1R genotype

Whole‐genome sequencing of matched germline and tumour pairs in a well‐characterized cohort of melanoma patients allowed investigation of associations between melanoma body site, age at melanoma onset and MC1R variant status with overall mutation burden and specific base pair changes observed in the corresponding melanoma. We observed statistically significant associations between mutation burden in melanoma and body site, age at onset and MC1R genotype, for both ultraviolet radiation (UVR) signature changes (C>T and CC>TT) and non‐UVR base pair substitutions, as well as with overall variant load.     

Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome

We provide phylogenetic analyses for primary Reptilia lineages including, for the first time, Sphenodon punctatus (tuatara) using data from whole mitochondrial genomes. Our analyses firmly support a sister relationship between Sphenodon and Squamata, which includes lizards and snakes. Using Sphenodon as an outgroup for select squamates, we found evidence indicating a sister relationship, among our study taxa, between Serpentes (represented by Dinodon) and Varanidae. Our analyses support monophyly of Archosauria, and a sister relationship between turtles and archosaurs. This latter relationship is congruent with a growing set of morphological and molecular analyses placing turtles within crown Diapsida and recognizing them as secondarily anapsid (lacking a skull fenestration). Inclusion of Sphenodon, as the only surviving member of Sphenodontia (with fossils from the mid-Triassic), helps to fill a sampling gap within previous analyses of reptilian phylogeny. We also report a unique configuration for the mitochondrial genome of Sphenodon, including two tRNA(Lys) copies and an absence of ND5, tRNA(His), and tRNA(Thr) genes.     

Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens

New quantitative methods are applied to the 135 human mitochondrial sequences from the Vigilant et al. data set. General problems in analyzing large numbers of short sequences are discussed, and an improved strategy is suggested. A key feature is to focus not on individual trees but on the general "landscape" of trees. Over 1,000 searches were made from random starting trees with only one tree (a local optimum) being retained each time, thereby ensuring optima were found independently. A new tree comparison metric was developed that is unaffected by rearrangements of trees around many very short internal edges. Use of this metric showed that downweighting hypervariable sites revealed more evolutionary structure than studies that weighted all sites equally. Our results are consistent with convergence toward a global optimum. Crucial features are that the best optima show very strong regional differentiation, a common group of 49 African sequences is found in all the best optima, and the best optima contain the 16 !Kung sequences in a separate group of San people. The other 86 sequences form a heterogeneous mixture of Africans, Europeans, Australopapuans, and Asians. Thus all major human lineages occur in Africa, but only a subset occurs in the rest of the world. The existence of these African-only groups strongly contradicts multiregional theories for the origin of Homo sapiens that require widespread migration and interbreeding over the entire range of H. erectus. Only when the multiregional model is rejected is it appropriate to consider the root, based on a single locus, to be the center of origin of a population (otherwise different loci could give alternative geographic positions for the root). For this data, several methods locate the root within the group of 49 African sequences and are thus consistent with the recent African origin of H. sapiens. We demonstrate that the time of the last common ancestor cannot be the time of major expansion in human numbers, and our results are thus also consistent with recent models that differentiate between the last common ancestor, expansion out of Africa, and the major expansion in human populations. Such a two-phase model is consistent with a wide range of molecular and archeological evidence.      

Stereochemical requirements of alpha 2-adrenergic receptors for alpha-methyl substituted phenethylamines

The alpha 1- and alpha 2-adrenergic effects of the stereoisomers of alpha-methyldopamine were evaluated in guinea pig aorta and field-stimulated guinea pig ileum, respectively, in order to establish the stereochemical requirements of these receptors for alpha-methyl substituted phenethylamines. The alpha 1-adrenergic receptor did not distinguish between the stereoisomers of alpha-methyldopamine which is in marked contrast to the alpha 2-adrenergic receptor where a dramatic stereochemical preference for the 2S(+)-isomer was observed. In addition, 2R(-)-alpha-methyldopamine displayed no alpha-receptor subtype specificity whereas 2S(+)-alpha-methyldopamine was highly selective (23 fold) for the alpha 2-adrenergic receptor. These results indicate that the alpha 2-adrenergic receptor can recognize and accept methyl substituents at the alpha-carbon atom of phenethylamines when correctly oriented, while the alpha 1-adrenergic receptor cannot. Thus, the alpha-carbon atom is a major determinant of the alpha 2-adrenergic effects of phenethylamines, and plays an important role in determining alpha-receptor subtype specificity. It is hypothesized that the alpha 2-adrenergic receptor (but not alpha 1) has an additional recognition site which will accommodate alpha-substituted phenethylamines.     

Isoflavone,wax and triterpene constituents of Wyethia mollis

The hexane extract of Wyethia mollis contains the n-alkanes C₁₅-C₁₈, C₂₀-C₂₅, C₂₇ and C₂₉. Linoleic acid was the only detectable acidic component. A mass spectral analysis of the wax ester fraction indicated that it was a mixture of homologues, the saturated even-carbon acids n-C₁₆-C₃₀ esterfield with the saturated even-carbon alcohols n-C₁₈-C₂₆. The chloroform extract yielded the known isoflavones santal and 3′-O-methylorobol along with a new lanostane-type triterpene, 22,25-epoxy-lanosta-7:9(11)-dien-3-one. The wide distribution of n-alkanes and the decreased odd-even carbon ratio are consistent with the proposed primitive nature of this plant.     

Glandular prediction: the pride and the prejudice

For the cytologist and clinician alike, glandular lesions pose possibly the greatest challenge in cervical screening. Worldwide, with increasing confidence in cytological prediction, terminology is evolving. In the UK, with the adoption of liquid based methods, the technical aspects of cervical cytology are being addressed, it is now time to standardise our terminology in glandular reporting. Consideration of the cytological complexity, clinical needs and international protocols is essential in this endeavour.     

The effects of progesterone supplementation on the metabolic clearance rate of progesterone in the pregnant rat

In the pregnant rat, short-term stability of progesterone blood concentrations may involve an active homeostatic mechanism. In the present study, we examined the possibility that the metabolic clearance rate (MCR) of progesterone can respond to a change in progesterone production and thus reduce variation in blood concentrations. Progesterone was administered both acutely and chronically to conscious rats, and the effective production rate, MCR, and blood concentration were monitored on Day 16 of pregnancy. Acute, low-dose progesterone supplementation, which effectively raised production rate by 29%, had no effect on the MCR of progesterone. Acute, high-dose supplementation, which raised total progesterone production by 68%, caused a 35% fall in the MCR of progesterone. Chronically supplemented rats received s.c. injections of progesterone (20 mg) once daily over Days 13-16 of pregnancy. The resultant production rate measured on Day 16 was 114% higher than that in controls, but there was no difference in MCR. Collectively, these experiments demonstrate that no short-term homeostatic mechanism involving the MCR operates to control blood progesterone concentrations in Day 16 pregnant rats. Thus, progesterone homeostasis appears limited to long-term developmental changes rather than short-term physiological control.