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.      

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.      

Heat shock response of germinating embryos of wheat : effects of imbibition time and seed vigor

Seeds frequently face a hostile environment during early germination. In order to determine whether seeds have evolved unique mechanisms to deal with such environments, a survey of the heat shock response in isolated embryos of wheat (Triticum aestivum L.) was undertaken. Embryos simultaneously heat shocked and labeled following several different periods of prior imbibition up to 12 hours synthesized many groups of heat shock proteins (hsps) typical of other plant and animal systems. Also, five developmentally dependent hsps, present only in treatments imbibed less than 6 hours prior to heat shock, were detected. These proteins have relative molecular masses of 14, 40, 46, 58, and 60 kilodaltons. One of the developmentally dependent hsps is among the most highly labeled hsps found in early imbibed embryos. The possibility that this protein is the E_m protein is discussed. The hypothesis that the capacity for hsp synthesis is affected by seed vigor was also tested. The heat shock responses of embryos from two high and two low vigor seed lots were compared using one- and two-dimensional electrophoresis of labelled protein extracts. The results indicate that both of the low vigor lots tested had weaker heat shock responses than their high vigor counterparts overall. Not all hsps were relatively less abundant in low vigor embryos. The developmentally dependent hsps showed little relationship to vigor. Some of the developmentally dependent hsps were actually made in greater amounts, relative to other proteins, in the low vigor seed lots. The results presented here demonstrate that imbibing embryos are capable of expressing an enhanced heat shock response, and that this response is related to seed vigor.     

Peak dynamic force in human gait

Studies were made of the forces generated at heel stroke in human gait using both force plates having a high resonant frequencies (capable of picking up high frequency components in the contact force) as well as a force transducer inserted into the heel of the shoe of the subjects. The output traces were analyzed for the existence of high frequency impulsive loads during a normal walking cycle. The effect of the complicance of the foot and floor was studied with the force transducers. The results showed that during normal human gait the lower limb is subjected to a high frequency impulsive load at heel strike. The severity of this impulse varied with the individual, the velocity and angle with which the limb aproached the ground and the compliance of the two materials coming in contact at heel strike. The magnitude of this peak force varied from 0.5 to 1.25 times body weight and its frequency components from 10 to 75 Hz.     

Purification and characterization of a UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase specific for glycosylation of threonine residues.

A UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase from porcine submaxillary glands was purified to electrophoretic homogeneity. IgG prepared from antisera against the pure enzyme immunoprecipitated the transferase in Triton X-100 extracts of submaxillary glands. The submaxillary transferase is a membrane-bound enzyme in contrast to the pure bovine colostrum enzyme, which is soluble in the absence of detergents. Both transferases have similar properties but also differ significantly. Examination of the acceptor substrate specificity of the submaxillary gland transferase showed that it specifically transferred N-acetylgalactosamine from UDP-GalNAc to the hydroxyl group of threonine and was devoid of transferase activity toward serine-containing peptides. These results imply that more than one transferase is involved in forming the GalNAc-threonine and the GalNAc-serine linkages found in O-linked oligosaccharides in glycoproteins. The amino acid sequence adjacent to glycosylated threonine residues may influence the rate of glycosylation by the pure transferase. For example, the second threonine residue in the sequence, Thr-Thr, appears to be glycosylated about twice as fast as the first and more rapidly than single, isolated threonine residues. However, no unique consensus sequence for glycosylation of threonine residues is evident, and any accessible threonine residue appears to be a potential acceptor substrate.     

Randomised controlled trial of intravenous antibiotic treatment for cellulitis at home compared with hospital

Objectives To compare the efficacy, safety, and acceptability of treatment with intravenous antibiotics for cellulitis at home and in hospital.Design Prospective randomised controlled trial.Setting Christchurch, New Zealand.Participants 200 patients presenting or referred to the only emergency department in Christchurch who were thought to require intravenous antibiotic treatment for cellulitis and who did not have any contraindications to home care were randomly assigned to receive treatment either at home or in hospital.Main outcome measures Days to no advancement of cellulitis was the primary outcome measure. Days on intravenous and oral antibiotics, days in hospital or in the home care programme, complications, degree of functioning and pain, and satisfaction with site of care were also recorded.Results The two treatment groups did not differ significantly for the primary outcome of days to no advancement of cellulitis, with a mean of 1.50 days (SD 0.11) for the group receiving treatment at home and 1.49 days (SD 0.10) for the group receiving treatment in hospital (mean difference 0.01 days, 95% confidence interval -0.3 to 0.28). None of the other outcome measures differed significantly except for patients'' satisfaction, which was greater in patients treated at home.Conclusions Treatment of cellulitis requiring intravenous antibiotics can be safely delivered at home. Patients prefer home treatment, but in this study only about one third of patients presenting at hospital for intravenous treatment of cellulitis were considered suitable for home treatment.