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.      

Preparation of Antimicrobial Compounds by Hydrolysis of Oleuropein from Green Olives

Oleuropein, an intensely bitter glucoside, was isolated from green olives. Hydrolysis products obtained from oleuropein in sufficient quantity for further tests were: (i) beta-3,4-dihydroxyphenylethyl alcohol prepared by acid hydrolysis of oleuropein; (ii) elenolic acid obtained by methanolysis of oleuropein, isolation of the intermediate acetal, and subsequent acid hydrolysis; and (iii) oleuropein aglycone formed by the action of beta-glucosidase on the parent glucoside. Mass spectral verification of the isolated compounds and ultraviolet absorption data are given. Oleuropein and its aglycone had similar threshold levels for detection of bitterness, whereas elenolic acid and beta-3,4-dihydroxyphenylethyl alcohol were not judged to be bitter.     

Antimicrobial Properties of Oleuropein and Products of Its Hydrolysis from Green Olives

Oleuropein, the bitter glucoside in green olives, and products of its hydrolysis were tested for antibacterial action against certain species of lactic acid bacteria involved in the brine fermentation of olives. Oleuropein was not inhibitory, but two of its hydrolysis products, the aglycone and elenolic acid, inhibited growth of the four species of lactic acid bacteria tested. Another hydrolysis product, beta-3,4-dihydroxyphenylethyl alcohol, was not inhibitory. The aglycone of oleuropein and elenolic acid were much more inhibitory when the broth medium contained 5% NaCl; 150 mug of either compound per ml prevented growth of Lactobacillus plantarum. A crude extract of oleuropein, tested by paper disk bioassay, was inhibitory to 3 of 17 species of bacteria screened, none of which were lactic acid bacteria. The acid hydrolysate of the extract was inhibitory to 11 of the bacteria, which included four species of lactic acid bacteria and other gram-positive and gram-negative species. Neither crude preparation was inhibitory to growth of the seven species of yeasts tested. A possible explanation is given for the previously reported observation that heating (3 min, 74 C) olives prior to brining renders them more fermentable by lactic acid bacteria. Results of a brining experiment indicated that oleuropein is degraded to antibacterial compounds when unheated olives are brined.     

Microbial inhibition by an isolate of pediococcus from cucumber brines

We reported earlier that Pediococcus cerevisiae FBB-61 inhibited Lactobacillus plantarum FBB-67 in mixed species inoculation used for the fermentation of brined cucumbers. Herein, 16 isolates of the Pediococcus genus from various sources were tested for inhibitory activity against L. plantarum and other microorganisms by a seeded-agar screening technique. Only two of the 16 isolates gave consistent and distinctive zones of inhibition, and both were isolated from fermenting cucumber brines on separate occasions. These two isolates did not inhibit each other but did inhibit the other 14 Pediococcus isolates in addition to L. plantarum. They also inhibited several other gram-positive bacteria, but not four species each of gram-negative bacteria and yeasts tested. Inoculation of cucumber juice broth with P. cerevisiae FBB-61 and L. plantarum WSO resulted in a drastic reduction in the plate count of L. plantarum WSO during day 1, but counts increased rapidly thereafter. Consequently, acid production by L. plantarum WSO was delayed. Noninhibitory isolates of Pediococcus had no appreciable effect on growth and acid production by L. plantarum WSO.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Widespread and ancient distribution of a noncanonical genetic code in diplomonads

Recently, a group of diplomonads has been found to use a genetic code in which TAA and TAG encode glutamine rather than termination. To survey the distribution of this characteristic in diplomonads, we sought to identify TAA and TAG codons at positions where glutamine is expected in genes for alpha-tubulin, elongation factor-1 alpha, and the gamma subunit of eukaryotic translation initiation factor-2. These sequences show that the variant genetic code is utilized by almost all diplomonads, with the genus Giardia alone using the universal genetic code. Comparative phylogenetic analysis reveals that the switch to this genetic code took place very early in the evolution of diplomonads and was likely a single event. Termination signals and downstream untranslated regions were also cloned from three Hexamita genes. In all three of these genes, the predicted TGA termination codon was found at the expected position. Interestingly, the untranslated regions of these genes are high in AT. This is incongruent with the coding regions, which are comparatively GC-rich.      

Bioethics for clinicians: 2. Disclosure.

In the context of patient consent, "disclosure" refers to the provision of relevant information by the clinician and its comprehension by the patient. Both elements are necessary for valid consent. Disclosure should inform the patient adequately about the treatment and its expected effects, relevant alternative options and their benefits and risks, and the consequences of declining or delaying treatment. The clinician''s goal is to disclose information that a reasonable person in the patient''s position would need in order to make an informed decision. Therefore, clinicians may need to consider how the proposed treatment (and other options) might affect the patient''s employment, finances, family life and other personal concerns. Clinicians may also need to be sensitive to cultural and religious beliefs that can affect disclosure.     

Trophic ecology and persistence of invasive silver carp Hypophthalmichthys molitrix in an oligotrophic South African impoundment

The alien invasive silver carp Hypophthalmichthys molitrix established a self-sustaining feral population in an oligotrophic impoundment, Flag Boshielo Dam, in South Africa. The ability of this population to persist in a dam with low algal biomass (median annual suspended chlorophyll a = 0.08 µg l^?1), and limited access to rivers considered large enough for successful spawning, has implications for their invasive potential in other systems. Stomach content and stable isotope analysis were used to assess the trophic ecology of H. molitrix, which was then compared with indigenous Mozambique tilapia Oreochromis mossambicus, on a seasonal basis during 2011. Hypophthalmichthys molitrix are generalist filter feeders, with a diet consisting primarily of sediment, vegetative detritus, dinoflagellates and diatoms. The dominance of sediments in their stomachs suggests occasional benthic scavenging. However, H. molitrix occupied a higher trophic level (TL = 2.8) than expected, suggesting that this population subsidised their diet with an unidentified dietary constituent, characterised by enriched nitrogen values. Although the stomach contents indicated dietary overlap between H. molitrix and O. mossambicus, stable isotopes revealed fine-scale resource partitioning, despite both species occupying the same trophic level. Nonetheless, the persistence of this feral H. molitrix population in an oligotrophic impoundment highlights their phenotypic plasticity.