Using Haplotype Trees for Phylogeographic and Species Inference in Fish Populations

Genetic variation is now routinely screened at the DNA sequence level in many studies. If the DNA region being screened has not experienced excessive amounts of recombination, it is often possible to reconstruct the evolutionary history of the genetic variation in the form of a haplotype tree. This tree estimates the evolutionary pathway that interconnects all the different haplotypes (sequence variants) observed in the sample. This haplotype tree can be used to define a series of nested branches (clades) that reflects the relative temporal history of the haplotypes and groups of haplotypes. Geographical information can then be overlaid upon this temporal series to test for significant associations between geography and temporal position in the haplotype tree. This allows a reconstruction of how the genetic variation arose and spread in both space and time. Such reconstructions can yield many insights into the joint roles of recurrent events such as gene flow and of historical events such as fragmentation or range expansion. These points are illustrated with studies on the chub, Leuciscus cephalus. There is also a need to extend such nested phylogeographic analyses to a phylo/reticulate geographic analysis that incorporates both assortment and recombination between and within DNA regions. A preliminary phylo/reticulate geographic analysis is presented of the transferrin locus in the brown trout, Salmo trutta, species complex that reveals the importance of hybridization in the recent evolutionary history of this group. This example shows the inadequacy of a strictly phylogenetic approach and illustrates the need to incorporate reticulate evolution. The results of nested clade phylogeographic analysis and the new phylo/reticulate geographic analysis are then used for inferring species status of the marbled trout. The results indicate that an old hybridization event may have played a role in the origin of the marbled trout. Currently the marbled trout is primarily endangered by hybridization with introduced brown trout. These results show both the positive and negative impacts of hybridization upon biodiversity. Such phylo/reticulate geographic studies will challenge both our concepts of species and our conservation management strategies.     

Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain

Sulfur bacteria such as Beggiatoa or Thiomargarita have a particularly high capacity for storage because of their large size. In addition to sulfur and nitrate, these bacteria also store phosphorus in the form of polyphosphate. Thiomargarita namibiensis has been shown to release phosphate from internally stored polyphosphate in pulses creating steep peaks of phosphate in the sediment and thereby inducing the precipitation of phosphorus-rich minerals. Large sulfur bacteria populate sediments at the sites of recent phosphorite formation and are found as fossils in ancient phosphorite deposits. Therefore, it can be assumed that this physiology contributes to the removal of bioavailable phosphorus from the marine system and thus is important for the global phosphorus cycle. We investigated under defined laboratory conditions which parameters stimulate the decomposition of polyphosphate and the release of phosphate in a marine Beggiatoa strain. Initially, we tested phosphate release in response to anoxia and high concentrations of acetate, because acetate is described as the relevant stimulus for phosphate release in activated sludge. To our surprise, the Beggiatoa strain did not release phosphate in response to this treatment. Instead, we could clearly show that increasing sulfide concentrations and anoxia resulted in a decomposition of polyphosphate. This physiological reaction is a yet unknown mode of bacterial polyphosphate usage and provides a new explanation for high phosphate concentrations in sulfidic marine sediments.     

O-acetyl-salicylic acid promotes colony formation from protoplasts of an elite maize inbred

The salicylic acid derivative acetylsalicylic acid (ASA) was found to promote colony formation from protoplasts isolated from embryogenic suspension cultures of an elite maize inbred line. The drug was most effective at concentrations of 30–100 mg/l, and increases of more than 20-fold in the number of colonies recovered from protoplasts were obtained. The rate of growth of protoplast-derived cell colonies was not affected.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - DMSO dimethylsulfoxide - KM Kao and Michayluk medium (1975) - MES 2[N-morpholino]ethanesulfonic acid - ASA acetylsalicylic acid     

Interleukin inhibition by a parasite proteinase inhibitor, taeniaestatin

A proteinase inhibitor, taeniaestatin, isolated from the larval stage of the cestode Taenia taeniaeformis inhibits endogenous IL 2 generation in murine lymphocytes and IL 1 induced proliferation of murine thymocytes in a dose-dependent manner. However, taeniaestatin does not inhibit exogenous IL 2-induced proliferation of an IL 2-dependent cell line at any dose tested. These data indicate that the lack of IL 2 generation may be due in part to inhibition of a crucial cell-associated proteinase subsequent to cellular activation, or the lack of an effective IL 2 signal for differentiation. Our results are novel findings concerning molecular pathways for parasite inhibition of host immune responses, and suggest that selected proteinase inhibitors may be useful in clinical situations in which IL 1 or IL 2 are elevated.     

Reaction rate measurements of proteases and glycosidases with chromogenic methods

Simultaneous azo-coupling and indigogenic methods were evaluated for the quantitative histochemical assay of the plasma membrane proteases gamma-glutamyl transpeptidase (EC 2.3.2.2) and dipeptidyl peptidase IV (EC 3.4.14.5) and the glycosidases maltase-glucoamylase and glucoamylase (EC 3.2.1.20) in decidual cells, jejunal enterocytes and renal proximal tubulocytes. Using kinetic (continuous) microdensitometry, a linear increase in the final reaction product was found from 3 up to 10 min, depending on the substrate concentration and the plasma membrane glycosidase or protease under investigation. Combined continuous and end point (static) microdensitometry revealed a linear relationship between the section thickness (enzyme concentration) and final reaction product up to 12 microns for the proteases and up to 16 microns for the glycosidases. Apparent Km and Vmax values were calculated with a computerized version of the direct linear plot and compared with the results obtained with the linear transformations according to Lineweaver-Burk, Eadie-Hofstee and Hanes. Apparent Km and Vmax values for the proteases were calculated separately for each animal and were 1.82 mM and 1.02 mM and 2.43 arbitrary units (a.u.) and 1.67 a.u. (gamma-glutamyl transpeptidase, decidua) and 0.42 mM and 0.38 mM and 0.29 and 0.26 a.u. (dipeptidyl peptidase IV, decidua). For the alpha-D-glucosidases, the corresponding values were 0.23 mM and 0.15 a.u. (kidney) and 0.55 mM and 0.20 a.u. (jejunum). The results show the suitability of the indigogenic methods for quantitative histochemical measurements of plasma membrane alpha-D-glucosidases, whereas the simultaneous azo-coupling procedures seemed to be less suitable for the quantification of surface membrane proteases, due to, for example, interactions of diazonium salts with amino acid or peptide substrates, reaction products and peptide activators.     

Proliferation of AXC/SSh rat prostate cancer cells in vitro is androgen modulated

We used heterogeneous parental cultures of AXC/SSh rat prostate cancer cells to isolate clonally derived prostate cancer cell lines. Light and electron microscopic analyses established that parental and clonally isolated cells possess features characteristic of secretory epithelium. Biochemical analyses showed that these cells contained androgen receptors and acid phosphatase and 5 alpha-reductase activity; phenotypic markers characteristic of differentiated prostate epithelium. Content of these prostate epithelial cell markers was variable and cell line specific. We used selected cell lines to examine androgen modulation of AXC/SSh rat prostate cancer cell proliferation in vitro. We found that proliferation of C-family or D-family cells, those respectively maintained on medium without additions or medium containing 10(-7) M 5 alpha-dihydrotestosterone, was not affected by changes in medium testosterone concentration through the range 10(-6)-10(-9) M. In contrast, testosterone modified proliferation of T-family cells, those maintained on medium containing 10(-7) M testosterone, and effects were antagonized by the anti-androgen RU 23908. Preliminary studies established that AXC/SSh rat prostate cancer cells elaborate polypeptide components which stimulate in vitro cell proliferation. Both the ability to elaborate these components and their effects on in vitro cell proliferation appeared to be cell line specific.     

Renal cortical intermediary metabolism in the recovery phase of postischemic acute renal failure in the dog.

Renal metabolism has been studied in eight dogs before and 48 hr after a 60-min period of renal ischemia induced by clamping the left renal artery with the simultaneous removal of the right kidney, and in 12 sham-operated animals. The study involved the measurement of renal uptake and production of lactate, glutamine, glutamate, alanine, ammonium, and oxygen, and the measurement of the tissue concentrations of ATP, glutamine, lactate, alpha-ketoglutarate, aspartate, and alanine in the renal cortex. Two days after a temporary renal ischemia, the remaining kidney showed a 22% decrease in glomerular filtration rate (GFR) and a 25% decrease in renal plasma flow. Fractional sodium and potassium excretions were similar to those of control dogs. Renal production or extraction of glutamine, glutamate, alanine, ammonium, and oxygen (all expressed by 100 ml of GFR) was not significantly different in basal conditions or 2 days after ischemia, but lactate extraction was reduced in postischemic kidneys (-101 +/- 29 vs -204 +/- 38 mumol/100 ml GFR in control dogs). The cortical concentrations of glutamine and glutamate were lower in postischemic than in control kidneys. No differences were found in cortical concentration of alpha-ketoglutarate, aspartate, lactate, pyruvate, or ATP, but total nucleotides and inorganic phosphate were decreased in postischemic kidneys. It is concluded that in the recovery phase of the ischemia, a decreased lactate uptake is the main metabolic change, and total ATP production is adapted to the decrease of GFR and sodium reabsorption.