Phylogeny and classification of Rosaceae

Phylogenetic relationships among 88 genera of Rosaceae were investigated using nucleotide sequence data from six nuclear (18S, gbssi1, gbssi2, ITS, pgip, and ppo) and four chloroplast (matK, ndhF, rbcL, and trnL-trnF) regions, separately and in various combinations, with parsimony and likelihood-based Bayesian approaches. The results were used to examine evolution of non-molecular characters and to develop a new phylogenetically based infrafamilial classification. As in previous molecular phylogenetic analyses of the family, we found strong support for monophyly of groups corresponding closely to many previously recognized tribes and subfamilies, but no previous classification was entirely supported, and relationships among the strongly supported clades were weakly resolved and/or conflicted between some data sets. We recognize three subfamilies in Rosaceae: Rosoideae, including Filipendula, Rubus, Rosa, and three tribes; Dryadoideae, comprising the four actinorhizal genera; and Spiraeoideae, comprising Lyonothamnus and seven tribes. All genera previously assigned to Amygdaloideae and Maloideae are included in Spiraeoideae. Three supertribes, one in Rosoideae and two in Spiraeoideae, are recognized.     

Assessment of prolactin secretion in children: a profile of circadian prolactin secretion and the principles for interpreting it

INTRODUCTION: Prolactin (Prl) is secreted in a circadian pattern, although no method of interpreting it has yet been established. The aim of the study was to assess Prl secretion in children on the basis of the Prl circadian profile and to establish principles for the interpretation of the results obtained by this method. MATERIAL AND METHODS: The analysis comprised 41 healthy short children (25 boys); aged 5.2-16.3 years, in whom hormonal disorders and chronic diseases had been excluded. The children were divided into prepubertal or pubertal subgroups. Serum Prl concentrations were measured every 3 hours for 24 hours. To assess the rhythm the parameters of macroscopic analysis were calculated and receiver operating characteristic (ROC) analysis was performed. The group for comparison consisted of 30 children aged 8.9-17.2 years with hyperprolactinaemia. RESULTS: In each subgroup significantly higher Prl concentrations were observed at night than by day. No statistical differences were noticed between the groups regarding Prl concentrations at particular time points or parameter values during circadian Prl rhythm evaluation. In the group analysed weak correlations were found between age and Prl peak and trough levels. On the basis of ROC analysis criteria for the existence of normal circadian Prl rhythm in children were established. CONCLUSIONS: 1. The presence of normal circadian Prl rhythm is observed if at least one of the following three criteria is fulfilled: amplitude >1.8779; X(n)/X(d) ratio >1.685; regression index <-0.4107. 2. No interpretation in relation to sex, age and stage of puberty is necessary for the circadian prolactin secretion rhythm in children.     

Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals

In mammals there is a bias in amino acid usage near splice sites that is explained, in large part, by the high density of exonic splicing enhancers (ESEs) in these regions. Is there a similar bias for the relative use of synonymous codons, and can any such bias be predicted by their abundance in ESEs? Prior reports suggested that such trends may exist. From analysis of human exons, we find that 47 of the 59 codons with at least one synonym show differential usage in the proximity of exon ends, of which 42 remain significant after correction for multiple testing. Within sets of synonymous codons those more preferred near splice sites are generally those that are relatively more abundant within the ESEs. However, the examples given previously appear exceptionally good fits and there exist many exceptions, the usage of lysine's codons being a case in point. Similar results are observed in mouse exons. We conclude that splice regulation impacts on the choice of synonymous codons in mammals, but the magnitude of this effect is less than might at first have been supposed.     

History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation

Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the 2 populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another and are consistent with relatively deep linguistic divergence among the respective click languages.     

Trifolium pratense isoflavones in the treatment of menopausal hot flushes: A systematic review and meta-analysis

OBJECTIVE: To critically assess the evidence of supplements containing Trifolium pratense (red clover) isoflavones in the reduction of hot flush frequency in menopausal women. DATA SOURCES: Systematic literature searches were performed in (Medline (1951 - April 2006), Embase (1974 - April 2006), CINAHL (1982 - April 2006), Amed (1985 - April 2006) and The Cochrane Library (Issue 2, 2006). Reference lists located were checked for further relevant publications. Experts in the field and manufacturers of identified products were contacted for unpublished material. No language restrictions were imposed. REVIEW METHODS: Studies were selected according to predefined inclusion and exclusion criteria. All randomized clinical trials of monopreparations containing T. pratense isoflavones for treating hot flushes were included. Study selection, data extraction and validation were performed by at least two reviewers with disagreements being settled by discussion. Weighted means and 95% confidence intervals were calculated and sensitivity analyses were performed. RESULTS: Seventeen potentially relevant articles were retrieved for further evaluation. Five were suitable for inclusion in the meta-analysis. The meta-analysis indicates a reduction in hot flush frequency in the active treatment group (40-82 mg daily) compared with the placebo group (weighted mean difference -1.5 hot flushes daily; 95% CI -2.94 to 0.03; p=0.05). CONCLUSION: There is evidence of a marginally significant effect of T. pratense isoflavones for treating hot flushes in menopausal women. Whether the size of this effect can be considered clinically relevant is unclear. Whereas there is no apparent evidence of adverse events during short-term use, there are no available data on the safety of long-term administration.     

Identification of (η6-arene)ruthenium(II) protein binding sites in E. coli cells by combined multidimensional liquid chromatography and ESI tandem mass spectrometry: specific binding of [(η6- p -cymene)RuCl2(DMSO)] to stress-regulated proteins and to helicases

An automated multidimensional protein identification technology, which combines biphasic liquid chromatography with electrospray ionisation tandem mass spectrometry (MS/MS), was employed to analyse tryptic peptides from Escherichia coli cells treated with the antiproliferation agent [(η⁶-p-cymene)RuCl₂(DMSO)], where DMSO is dimethyl sulfoxide. MS/MS spectra were recorded for molecular ions generated by neutral loss of p-cymene from intensive peptide ions coordinated by the (η⁶-p-cymene)Ru^II fragment. Matching of the MS/MS spectra of the ruthenated peptides to spectra of proteins in the E. coli database enabled the identification of five protein targets for [(η⁶-p-cymene)RuCl₂(DMSO)]. One of these is the constitutive cold-shock protein cspC, which regulates the expression of genes encoding stress-response proteins, and three of the other targets, ppiD, osmY and sucC, are proteins of the latter type. The DNA damage-inducible helicase dinG was likewise established as a protein target. Aspartate carboxylate functions were identified as the probable Ru binding sites in cspC, ppiD and dinG, and threonine and lysine side chains in osmY and sucC, respectively. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effect of lactation stage and concurrent pregnancy on milk composition in the bottlenose dolphin

Although many toothed whales (Cetacea: Odontoceti) lactate for 2–3 years or more, it is not known whether milk composition is affected by lactation stage in any odontocete species. We collected 64 pooled milk samples spanning 1–30 months postpartum from three captive bottlenose dolphins Tursiops truncatus . Milks were assayed for water, fat, crude protein (TN × 6.38) and sugar; gross energy was calculated. Ovulation and pregnancy were determined via monitoring of milk progesterone. Based on analysis of changes in milk composition for each individual dolphin, there were significant increases ( P <0.05) in fat (in all three dolphins) and crude protein (in two of three), and a decrease ( P <0.05) in water (in two of three) over the course of lactation, but the sugar content did not change. In all three animals, the energy content was positively correlated with month of lactation, but the percentage of energy provided by crude protein declined slightly but significantly ( P <0.05). At mid-lactation (7–12 months postpartum, n =17), milk averaged 73.0±1.0% water, 12.8±1.0% fat, 8.9±0.5% crude protein, 1.0±0.1% sugar, 1.76±0.09 kcal g⁻¹ (=7.25 kJ g⁻¹) and 30.3±1.3% protein:energy per cent. This protein:energy per cent was surprisingly high compared with other cetaceans and in relation to the growth rates of calves. Milk progesterone indicated that dolphins ovulated and conceived between 413 and 673 days postpartum, following an increase in milk energy density. The significance of these observed compositional changes to calf nutrition will depend on the amounts of milk produced at different stages of lactation, and how milk composition and yield are influenced by sampling procedure, maternal diet and maternal condition, none of which are known.