New softwares for automated microsatellite marker development

Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence ‘experiment file’ format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.     

An experimental analysis of the effects of light and zooplankton on coral zonation

Summary In Panamá, vertical zonation of coral species is well marked; branching corals (Pocillopora spp.) predominate in shallow (1–6 m) water while massive forms (Pavona spp.) occupy the deeper (6–10 m) areas of the reef. To test the hypothesis that this zonation represents differential resource utilization (i.e., niche partitioning of food resources), one year manipulative field experiments were conducted at two depths (1 m and 7 m below Mean Lower Sea Level) assessing the relative contribution of light and zooplankton to the nutrition of three Pacific corals: Pocillopora damicornis, Pavona clavus and Pavona gigantea. Also tested were the related hypotheses that (i) energy for the maintenance and growth of corals comes mainly from light, independent of zooplankton supply and (ii) Porter's model, in which coral morphology is a predictor of the phototrophic-heterotrophic capabilities of a particular species. That is, corals with a branching morphology and a small polyp diameter (and short tentacle length) should be primarily phototrophic while those species with larger polyps and/or a massive form should show a greater degree of heterotrophy.The comparison of caged versus control corals indicated that the branching coral, Pocillopora damicornis (polyp diameter — 1 mm) grew independent of zooplankton supply (>95) but was markedly affected by shading. Pavona clavus (massive form with intermediate size polyps — 2 mm) was also negatively affected by shading but this effect was minimized when zooplankton was present. Surprisingly, under ambient light conditions, the growth of this specics was independent of zooplankton (>95); perhaps indicating a facultative reliance on zooplankton especially in shallow water. The third species, Pavona gigan-tea (massive form with largest polyps — 3 mm) was highly dependent on both light and zooplankton and was unable to compensate for the effects of shading by zooplankton feeding. This high dependence on light was unexpected since large polyps, according to Porter's model, would predict a more heterotrophic existence.Under all treatments, in both shallow and deep water, Pocillopora was found to grow more rapidly than either massive species. Thus, this study indicates that zonation on eastern Pacific reefs cannot be explained by depth-related differences in nutritional requirements among the species present. These results do provide the first long-term, experimental field evidence that corals are largely phototrophic organisms. The validity of Porter's model attempting to correlate phototrophic-heterotrophic abilities to morphological characteristics is, at least, partially verified: species with larger tentacles do appear to utilize zooplankton to a greater extent than those species with smaller tentacles. However, the significance of corallum morphology in predicting the mode of nutrient acquisition is unclear. Rather, behavioral patterns (tentacle expansion-contraction cycles) and location on the reef may be more important factors to consider.     

A new method to predict the epidemiology of fungal keratitis by monitoring the sales distribution of antifungal eye drops in Brazil

Purpose

Fungi are a major cause of keratitis, although few medications are licensed for their treatment. The aim of this study is to observe the variation in commercialisation of antifungal eye drops, and to predict the seasonal distribution of fungal keratitis in Brazil.

Methods

Data from a retrospective study of antifungal eye drops sales from the only pharmaceutical ophthalmologic laboratory, authorized to dispense them in Brazil (Opthalmos) were gathered. These data were correlated with geographic and seasonal distribution of fungal keratitis in Brazil between July 2002 and June 2008.

Results

A total of 26,087 antifungal eye drop units were sold, with a mean of 2.3 per patient. There was significant variation in antifungal sales during the year (p<0.01). A linear regression model displayed a significant association between reduced relative humidity and antifungal drug sales (R2 = 0.17,p<0.01).

Conclusions

Antifungal eye drops sales suggest that there is a seasonal distribution of fungal keratitis. A possible interpretation is that the third quarter of the year (a period when the climate is drier), when agricultural activity is more intense in Brazil, suggests a correlation with a higher incidence of fungal keratitis. A similar model could be applied to other diseases, that are managed with unique, or few, and monitorable medications to predict epidemiological aspects.     

Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture

Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolor M145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ΔphoP mutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures.     

ABCG1 influences the brain cholesterol biosynthetic pathway but does not affect amyloid precursor protein or apolipoprotein E metabolism in vivo

Cholesterol homeostasis is of emerging therapeutic importance for Alzheimer's disease (AD). Agonists of liver-X-receptors (LXRs) stimulate several genes that regulate cholesterol homeostasis, and synthetic LXR agonists decrease neuropathological and cognitive phenotypes in AD mouse models. The cholesterol transporter ABCG1 is LXR-responsive and highly expressed in brain. In vitro, conflicting reports exist as to whether ABCG1 promotes or impedes Abeta production. To clarify the in vivo roles of ABCG1 in Abeta metabolism and brain cholesterol homeostasis, we assessed neuropathological and cognitive outcome measures in PDAPP mice expressing excess transgenic ABCG1. A 6-fold increase in ABCG1 levels did not alter Abeta, amyloid, apolipoprotein E levels, cholesterol efflux, or cognitive performance in PDAPP mice. Furthermore, endogenous murine Abeta levels were unchanged in both ABCG1-overexpressing or ABCG1-deficient mice. These data argue against a direct role for ABCG1 in AD. However, excess ABCG1 is associated with decreased levels of sterol precursors and increased levels of SREBP-2 and HMG-CoA-reductase mRNA, whereas deficiency of ABCG1 leads to the opposite effects. Although functions for ABCG1 in cholesterol efflux and Abeta metabolism have been proposed based on results with cellular model systems, the in vivo role of this enigmatic transporter may be largely one of regulating the sterol biosynthetic pathway.     

Reversal of digestive interactions between Pacific reef corals: Mediation by sweeper tentacles

Summary Aggressive interactions among reef corals involving direct interference through extracoelenteric digestion has previously been considered as a potential mechanism for the maintenance of high species diversity. In this report I show that induced development of sweeper tentacles can reverse initial digestive interactions. In the eastern Pacific these reversals contribute to resource monopolization by fast growing pocilloporid corals. This suggests that other mechanisms must account for the maintenance of local species diversity.     

Toxoplasma gondii Chitinase Induces Macrophage Activation

Toxoplasma gondii is an obligate intracellular protozoan parasite found worldwide that is able to chronically infect almost all vertebrate species, especially birds and mammalians. Chitinases are essential to various biological processes, and some pathogens rely on chitinases for successful parasitization. Here, we purified and characterized a chitinase from T. gondii. The enzyme, provisionally named Tg_chitinase, has a molecular mass of 13.7 kDa and exhibits a Km of 0.34 mM and a Vmax of 2.64. The optimal environmental conditions for enzymatic function were at pH 4.0 and 50°C. Tg_chitinase was immunolocalized in the cytoplasm of highly virulent T. gondii RH strain tachyzoites, mainly at the apical extremity. Tg_chitinase induced macrophage activation as manifested by the production of high levels of pro-inflammatory cytokines, a pathogenic hallmark of T. gondii infection. In conclusion, to our knowledge, we describe for the first time a chitinase of T. gondii tachyzoites and provide evidence that this enzyme might influence the pathogenesis of T. gondii infection.     

An ion-exchange based extraction method for the detection of salmonellas in soil

A method that uses a cation-exchange resin (Chelex 100) and differential centrifugation for the extraction and detection of salmonellas in soil was developed. The extraction efficiencies of a range of materials were examined and Chelex plus polyethylene glycol was identified as the best combination. Shake speeds, shake times and differential centrifugation speeds were selected to give an optimum salmonella recovery. The Chelex method accurately enumerated 1 cell per 10 g of nonsterile soil within 24 h. Addition of glycerol to soil samples enabled storage at — 70°C for 85 d without significant decreases in salmonella numbers. The Oxoid Salmonella Rapid Test (SRT) could be used to pre-screen large numbers of soil samples for the presence of salmonellas, prior to analysis by the Chelex method. The SRT method detected Salmonella typhimurium at levels as low as 2·5 cells per 10 g of nonsterile soil.     

A Review: Synthesis of Aryl C-Glycosides Via the Heck Coupling Reaction

In this article, we focus on the synthesis of aryl C-glycosides via Heck coupling. It is organized based on the type of structures used in the assembly of the C-glycosides (also called C-nucleosides) with the following subsections: pyrimidine C-nucleosides, purine C-nucleosides, and monocyclic, bicyclic, and tetracyclic C-nucleosides. The reagents and conditions used for conducting the Heck coupling reactions are discussed. The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described.