Molecular characterization, technological properties and safety aspects of enterococci from 'Hussuwa', an African fermented sorghum product

AIMS: To identify enterococci from Hussuwa, a Sudanese fermented sorghum product, and determine their technological properties and safety for possible inclusion in a starter culture preparation. METHODS AND RESULTS: Twenty-two Enterococcus isolates from Hussuwa were identified as Enterococcus faecium by using phenotypic and genotypic tests such as 16S rDNA gene sequencing, RAPD-PCR and restriction fragment length polymorphism of the 16S/23S intergenic spacer region fingerprinting. Genotyping revealed that strains were not clonally related and exhibited a considerable degree of genomic diversity. Some strains possessed useful technological properties such as production of bacteriocins and H2O2 or utilization of raffinose and stachyose. None produced alpha-amylase or tannase. A safety investigation revealed that all strains were susceptible to the antibiotics ampicillin, gentamicin, chloramphenicol, tetracycline and streptomycin, but some were resistant to ciprofloxacin, erythromycin, penicillin and vancomycin. Production of biogenic amines or presence of genes encoding virulence determinants occurred in some strains. CONCLUSIONS: Enterococcus faecium strains are associated with fermentation of Sudanese Hussuwa. Some strains exhibited useful technological properties such as production of antimicrobial agents and fermentation of indigestible sugars, which may aid in stabilizing and improving the digestibility of the product respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Enterococci were shown to play a role in the fermentation of African foods. While beneficial properties of these bacteria are indicated, their presence in this food may also imply a hygienic risk as a result of antimicrobial resistances or presence of virulence determinants.     

ALOHOMORA: a tool for linkage analysis using 10K SNP array data

SUMMARY: ALOHOMORA is a software tool designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. Genotype data are converted into appropriate formats for a number of common linkage programs and subjected to standard quality control routines before linkage runs are started. ALOHOMORA is written in Perl and may be used to perform state-of-the-art linkage scans in small and large families with any genetic model. Options for using different genetic maps or ethnicity-specific allele frequencies are implemented. Graphic outputs of whole-genome multipoint LOD score values are provided for the entire dataset as well as for individual families. AVAILABILITY: ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see http://gmc.mdc-berlin.de/alohomora/     

Simulation of trait- and density-mediated indirect effects induced by piscivorous predators

The study demonstrates how to use a spatially explicit individual-based model (IBM) to tackle the problem of resolving density-mediated (DMII) and trait-mediated indirect interactions (TMII) when manipulative experimentation is difficult on the scale of community-level interactions in the real word. As an example we simulated predator-induced behavioural changes in a roach (Rutilus rutilus (L.)) population before and after stocking a lake with an additional pelagic predator (Sander lucioperca (L.)). By this it was possible to calculate bioenergetic gains and costs of trait changes as well as the relative proportions of DMIIs and TMIIs in roach consumption on littoral and pelagic resources in the lake food web. Despite higher net activity costs of 64%, roach migrating horizontally over the diel cycle had a net benefit (higher energy intake of 75%) compared to roach that were restricted to the littoral as a behavioural response to the new predator. By separating the components of the indirect predator effects, we demonstrate that a predator-induced modification in prey traits (behaviour, feeding activity) could contribute substantially to the net indirect effect of a predator even when there are strong density effects. When considering the predation pressure by roach on pelagic resources, the net TMIIs due to the behavioural adaptation of the consumer in response to the predator were 13–14 times stronger than the DMIIs alone. When comparing the different effects on littoral resources it can be shown that the TMIIs approximately compensate the DMIIs thus resulting in a nearly zero net effect.

Zusammenfassung

In der vorliegenden Arbeit wurde ein räumlich explizites individuenbasiertes Modell (IBM) verwendet, um dichteabhängige (DMII) und eigenschaftsabhängige (TMII) indirekte Interaktionen zu vergleichen. Da sich dies auf der Ebene der Lebensgemeinschaft unter realen experimentellen Bedingungen als besonders schwierig erwiesen hat, wurden räuberinduzierte Verhaltensänderungen einer Plötzenpopulation (Rutilus rutilus (L.)) vor und nach dem Besatz mit einem zusätzlichen pelagischen Räuber, dem Zander (Sander lucioperca (L.)), simuliert. Dadurch war es möglich, sowohl die energetischen Kosten und Nutzen der räuberinduzierten Verhaltensänderung als auch die relativen Anteile von DMIIs and TMIIs an der Plötzenkonsumtion auf litorale und pelagische Ressourcen innerhalb des Nahrungsnetzes zu kalkulieren. Verglichen mit den Plötzen, welche sich aufgrund des neuen Räubers vor allem im Litoral aufhielten, hatten die täglich (horizontal) wandernden Plötzen trotz höherer Nettoaktivitätskosten von 64% eine größere Energieaufnahme von 75%. Durch die Auflösung der verschiedenen indirekten Räubereffekte konnten wir demonstrieren, dass räuberinduzierte Modifikationen von Beuteeigenschaften (Verhalten, Fraßaktivität) erheblich zu den indirekten Nettoeffekten eines Räubers beitragen können, auch wenn starke dichteabhängige Effekte vorhanden sind. Wenn man die Plötzenkonsumtion auf pelagische Ressourcen betrachtet, so ergeben sich 13-14 fach stärkere TMIIs als DMIIs. Wenn man die verschiedenen Effekte auf litorale Ressourcen vergleicht, zeigt es sich, dass TMIIs die DMIIs kompensieren, wodurch der indirekte Nettoeffekt fast null beträgt.     

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis

In phylogenetic analyses with combined multigene or multiprotein data sets, accounting for differing evolutionary dynamics at different loci is essential for accurate tree prediction. Existing maximum likelihood (ML) and Bayesian approaches are computationally intensive. We present an alternative approach that is orders of magnitude faster. The method, Distance Rates (DistR), estimates rates based upon distances derived from gene/protein sequence data. Simulation studies indicate that this technique is accurate compared with other methods and robust to missing sequence data. The DistR method was applied to a fungal mitochondrial data set, and the rate estimates compared well to those obtained using existing ML and Bayesian approaches. Inclusion of the protein rates estimated from the DistR method into the ML calculation of trees as a branch length multiplier resulted in a significantly improved fit as measured by the Akaike Information Criterion (AIC). Furthermore, bootstrap support for the ML topology was significantly greater when protein rates were used, and some evident errors in the concatenated ML tree topology (i.e., without protein rates) were corrected. [Bayesian credible intervals; DistR method; multigene phylogeny; PHYML; rate heterogeneity.].     

A novel assay of cell rubidium uptake using graphite furnace atomic absorption: application to rats on a magnesium-deficient diet

The [Na,K]ATPase or sodium pump (SP) is a ubiquitous membrane cation transport system. Because of its potential participation in the pathophysiology of essential hypertension and cataract formation, the SP is under active investigation to detail its function and control. In this paper, we describe a novel, nonradioactive method of measuring SP ion transport activity in intact red blood cells (RBCs) using graphite furnace atomic absorption measurement of rubidium ion (Rb) uptake. This method provided sensitivity comparable to radioactive techniques, as assessed by experiments with human red blood cells (RBC) and ouabain, a known SP inhibitor, but this analytical approach eliminates the use of radioisotopes common to other Rb uptake assay methods. As a demonstration of its broader utility, the assay was used to assess the effects of dietary magnesium intake on SP-mediated ion transport in the RBCs of diet-controlled rats. Rats on 7 weeks of a magnesium-deficient (MgD) diet showed significant reductions in serum magnesium concentration, although levels remained in the lower region of the reference interval for healthy, magnesium replete animals. Red cell Rb uptake was significantly reduced in cells from the magnesium-restricted animals, demonstrating the sensitivity of Rb uptake to reduced magnesium intake, despite serum levels that fell within the reported normal range, and the utility of this Rb uptake assay in measuring physiological changes in SP function.     

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes

Between 1 and 1.5 billion years ago, eukaryotic organisms acquired the ability to convert light into chemical energy through endosymbiosis with a Cyanobacterium (e.g.,). This event gave rise to "primary" plastids, which are present in green plants, red algae, and glaucophytes ("Plantae" sensu Cavalier-Smith). The widely accepted view that primary plastids arose only once implies two predictions: (1) all plastids form a monophyletic group, as do (2) primary photosynthetic eukaryotes. Nonetheless, unequivocal support for both predictions is lacking (e.g.,). In this report, we present two phylogenomic analyses, with 50 genes from 16 plastid and 15 cyanobacterial genomes and with 143 nuclear genes from 34 eukaryotic species, respectively. The nuclear dataset includes new sequences from glaucophytes, the less-studied group of primary photosynthetic eukaryotes. We find significant support for both predictions. Taken together, our analyses provide the first strong support for a single endosymbiotic event that gave rise to primary photosynthetic eukaryotes, the Plantae. Because our dataset does not cover the entire eukaryotic diversity (but only four of six major groups in), further testing of the monophyly of Plantae should include representatives from eukaryotic lineages for which currently insufficient sequence information is available.     

Changes in Phenotype and Genotype of Austrian <Emphasis Type="BoldItalic">Salmo trutta</Emphasis> Populations during the Last Century

Synopsis We studied the phenotype and genotype of Austrian wild and hatchery Salmo trutta populations and compared with museum samples from the 19th century (1863--1909) using morphometric and genetic (RFLP of mtDNA) markers. We found significant differences between the populations from the 19th century, the current wild populations, and the hatchery populations in morphometric parameters (mainly shape of pectoral, ventral and anal fins) and the RFLP pattern of mtDNA. We could not find the typical phenotypes and genotypes from the 19th century in either of the current populations. This phenotypic and genotypic replacement is considered to be due to anthropogenic activities.     

Diversity and technological properties of predominant lactic acid bacteria from fermented cassava used for the preparation of Gari, a traditional African food

Traditional fermentation of cassava is dominated by a lactic acid bacteria (LAB) population. Fermentation is important for improving product flavour and aroma as well as safety, especially by reduction of its toxic cyanogenic glucosides. The production of Gari from cassava in Benin typically occurs on a household or small industrial scale, and consequently suffers from inconsistent product quality and may not always be safe for consumption. Therefore, the diversity of LAB from a typical cassava fermentation for the preparation of Gari, and their technologically relevant characteristics were investigated with a view towards selection of appropriate starter cultures. A total of 139 predominant strains isolated from fermenting cassava were identified using phenotypic tests and genotypic methods such as rep-PCR and RAPD-PCR. DNA-DNA hybridisation and sequencing of the 16S rRNA genes were done for selected strains. Lactobacillus plantarum was the most abundantly isolated species (54.6% of isolates), followed by Leuconostoc fallax (22.3%) and Lactobacillus fermentum (18.0%). Lactobacillus brevis, Leuconostoc pseudomesenteroides and Weissella paramesenteroides were sporadically isolated. The L. plantarum strains were shown to be better acid producers and capable of faster acid production than the L. fallax or L. fermentum strains. The incidence of beta-glucosidase (linamarase) activity was also highest among strains of this species. Production of antagonistic substances such as H2O2 and bacteriocins, however, was more common among L. fallax and L. fermentum strains. Strains of all three species were capable of utilising the indigestible sugars raffinose and stachyose. Therefore, a starter culture containing a mixture of strains from all three species was recommended.     

Non-thermal DNA breakage by mobile-phone radiation (1800 MHz) in human fibroblasts and in transformed GFSH-R17 rat granulosa cells in vitro

Cultured human diploid fibroblasts and cultured rat granulosa cells were exposed to intermittent and continuous radiofrequency electromagnetic fields (RF-EMF) used in mobile phones, with different specific absorption rates (SAR) and different mobile-phone modulations. DNA strand breaks were determined by means of the alkaline and neutral comet assay. RF-EMF exposure (1800 MHz; SAR 1.2 or 2 W/kg; different modulations; during 4, 16 and 24h; intermittent 5 min on/10 min off or continuous wave) induced DNA single- and double-strand breaks. Effects occurred after 16 h exposure in both cell types and after different mobile-phone modulations. The intermittent exposure showed a stronger effect in the comet assay than continuous exposure. Therefore we conclude that the induced DNA damage cannot be based on thermal effects.