Selecting representative model micro-organisms

Background  

Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.     

Different internal metabolites trigger the induction of glycolytic gene expression in Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae, the sugar-induced expression of various genes coding for glycolytic enzymes is triggered by increases in the concentrations of different internal metabolites. Here, we show that the induction of the glycolytic isoenzyme enolase 2 is strictly dependent on the abilities of different mutant strains to increase the level of glucose-6-phosphate after the addition of sugars. In contrast, the induction of alcohol dehydrogenase I is dependent on increasing concentrations of metabolites in the late stages of glycolysis.     

Modelling expected trout ranges under current and future water temperature regimes in the Eastern Cape,South Africa

Different values have resulted in conflicts between anglers and conservation lobbies in the management of trout in South Africa. Key to the conflict is the demarcation of boundaries to areas in which brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss currently occur, or are likely to establish following stocking for angling. To provide a longer-term perspective on these areas, we developed models to link salmonid biological thermal thresholds to elevation. These, when applied spatially using a digital elevation model with a probability of occurrence model, provided the basis for estimating potentially available thermal habitat for these two cold water species. Here, we acknowledge that other variables (stocking history; river connectivity) also play a role in understanding trout distributions. Using a simple scenario of an increase in mean daily water temperatures of 2 °C, we demonstrated that both brown and rainbow trout are likely to exhibit considerable range reductions in the future. Because it is possible that these range restrictions will result in an increasing desire to introduce trout into areas above their current distribution limits for the maintenance of angling opportunities, conservation managers should prioritise these areas, with management interventions seeking to understand what will help to limit introductions.     

Concurrent knock-out of at least 20 transporter genes is required to block uptake of hexoses in Saccharomyces cerevisiae

The hexose transporter family of Saccharomyces cerevisiae comprises 18 proteins (Hxt1-17, Gal2). Here, we demonstrate that all these proteins, except Hxt12, and additionally three members of the maltose transporter family (Agt1, Ydl247, Yjr160) are able to transport hexoses. In a yeast strain deleted for HXT1-17, GAL2, AGT1, YDL247w and YJR160c, glucose consumption and transport activity were completely abolished. However, as additional deletion of the glucose sensor gene SNF3 partially restored growth on hexoses, our data indicate the existence of even more proteins able to transport hexoses in yeast.     

Switching the mode of metabolism in the yeast Saccharomyces cerevisiae

The biochemistry of most metabolic pathways is conserved from bacteria to humans, although the control mechanisms are adapted to the needs of each cell type. Oxygen depletion commonly controls the switch from respiration to fermentation. However, Saccharomyces cerevisiae also controls that switch in response to the external glucose level. We have generated an S. cerevisiae strain in which glucose uptake is dependent on a chimeric hexose transporter mediating reduced sugar uptake. This strain shows a fully respiratory metabolism also at high glucose levels as seen for aerobic organisms, and switches to fermentation only when oxygen is lacking. These observations illustrate that manipulating a single step can alter the mode of metabolism. The novel yeast strain is an excellent tool to study the mechanisms underlying glucose-induced signal transduction.     

Polarity of peatmoss (Sphagnum) evolution: who says bryophytes have no roots?

The class Sphagnopsida (Bryophyta) includes two genera: Ambuchanania and Sphagnum. Ambuchanania contains just one rare species known from two Tasmanian localities, but Sphagnum comprises a speciose clade of mosses that dominates many wetland ecosystems, especially in the boreal zone of the Northern Hemisphere. Recent phylogenetic analyses have resolved well-supported clades within Sphagnum, but polarizing Sphagnum evolution has been problematic because the genus is so isolated that it is difficult to determine homologies between morphological and/or molecular traits within Sphagnum with those of any potential outgroup. DNA sequences from 16 genomic regions representing the mitochondrial, chloroplast, and nuclear genomes (ca. 16 kilobases) were obtained from 24 species of Sphagnum plus one species each from Takakia and Andreaea in order to resolve a rooted phylogeny. Two tropical species, S. sericeum and S. lapazense, were resolved as sister to the rest of the genus and are extremely divergent from all other sphagna. The main Sphagnum lineage consists of two clades; one includes the sections Sphagnum, Rigida, and Cuspidata, and the other includes Subsecunda, Acutifolia, and Squarrosa. The placement of section Subsecunda is weakly supported, but other nodes are strongly supported by maximum parsimony, maximum likelihood, and Bayesian analyses. In addition to homogeneous Bayesian analyses, heterogeneous models were employed to account for different patterns of nucleotide substitution among genomic regions.     

Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta)

Abstract Pleurocarpous mosses, characterized by lateral female gametangia and highly branched, interwoven stems, comprise three orders and some 5000 species, or almost half of all moss diversity. Recent phylogenetic analyses resolve the Ptychomniales as sister to the Hypnales plus Hookeriales. Species richness is highly asymmetric with approximately 100 Ptychomniales, 750 Hookeriales, and 4400 Hypnales. Chloroplast DNA (cpDNA) sequences were obtained to compare partitioning of molecular diversity among the orders with estimates of species richness, and to test the hypothesis that either the Hookeriales or Hypnales underwent a period (or periods) of exceptionally rapid diversification. Levels of biodiversity were quantified using explicitly historical "phylogenetic diversity" and non-historical estimates of standing sequence diversity. Diversification rates were visualized using lineage-through-time (LTT) plots, and statistical tests of alternative diversification models were performed using the methods of Paradis (1997). The effects of incomplete sampling on the shape of LTT plots and performance of statistical tests were investigated using simulated phylogenies with incomplete sampling. Despite a much larger number of accepted species, the Hypnales contain lower levels of (cpDNA) biodiversity than their sister group, the Hookeriales, based on all molecular measures. Simulations confirm previous results that incomplete sampling yields diversification patterns that appear to reflect a decreasing rate through time, even when the true phylogenies were simulated with constant rates. Comparisons between simulated results and empirical data indicate that a constant rate of diversification cannot be rejected for the Hookeriales. The Hypnales, however, appear to have undergone a period of exceptionally rapid diversification for the earliest 20% of their history.     

Presence of fungi in stool of children

A total of 258 children were tested for the presence of fungi in stool. One group consisted of 148 children with non-specific gastrointestinal tract disorders while the other was a group of 110 asthmatics. A quantitative method of enzymatic and mechanical homogenisation was used. The findings were divided into three ranges as follows: < 10(3), 10(3)-10(5), > 10(5) fungal cells in one gram of stool. The number of > 10(5) fungal cells in one gram of stool was considered as pathogenic and requiring treatment. Such a number of fungi in stool was found in 48.1% of children in the first group and in 35.9% in the second one. However, the percentage of fungal presence was higher in the group of asthmatics (83.6% vs. 70.3%). Candida albicans considerably outnumbered the remaining fungal species in the isolates. It was found out that other than C. albicans Candida species were more resistant to the antifungals.