Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors

Background  

The typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set.     

Unstirred water layers in rabbit intestine: effects of pectin

Pectins have been shown to affect the absorption of several different nutrients in clinical studies; however, the mechanisms for decreased absorption have not been defined. A possibility not studied with regards to pectin, but previously demonstrated to be important in absorption, is the effect of change in the unstirred water layer. As the unstirred water layer increases in thickness, the rate of absorption decreases for certain nutrients. The effect of pectin on the unstirred water layer in the lumen of rabbit jejunum was examined by previously described techniques. It was observed that: (1) increases in pectin concentration resulted in an increased thickness of the unstirred water layer; (2) for any stir rate, the addition of pectin increased the thickness of the unstirred water layer; and (3) stir rate is inversely related to the thickness of the unstirred water layer. It was concluded from these results that pectin increases the thickness of the unstirred water layer in rabbit jejunum. This mechanism may explain, in part, the reduction of the rate of absorption of certain nutrients seen following pectin ingestion.     

13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches

Conventional metabolic flux analysis uses the information gained from determination of measurable fluxes and a steady-state assumption for intracellular metabolites to calculate the metabolic fluxes in a given metabolic network. The determination of intracellular fluxes depends heavily on the correctness of the assumed stoichiometry including the presence of all reactions with a noticeable impact on the model metabolite balances. Determination of fluxes in complex metabolic networks often requires the inclusion of NADH and NADPH balances, which are subject to controversial debate. Transhydrogenation reactions that transfer reduction equivalents from NADH to NADPH or vice versa can usually not be included in the stoichiometric model, because they result in singularities in the stoichiometric matrix. However, it is the NADPH balance that, to a large extent, determines the calculated flux through the pentose phosphate pathway. Hence, wrong assumptions on the presence or activity of transhydrogenation reactions will result in wrong estimations of the intracellular flux distribution. Using 13C tracer experiments and NMR analysis, flux analysis can be performed on the basis of only well established stoichiometric equations and measurements of the labeling state of intracellular metabolites. Neither NADH/NADPH balancing nor assumptions on energy yields need to be included to determine the intracellular fluxes. Because metabolite balancing methods and the use of 13C labeling measurements are two different approaches to the determination of intracellular fluxes, both methods can be used to verify each other or to discuss the origin and significance of deviations in the results. Flux analysis based entirely on metabolite balancing and flux analysis, including labeling information, have been performed independently for a wild-type strain of Aspergillus oryzae producing alpha-amylase. Two different nitrogen sources, NH4+ and NO3-, have been used to investigate the influence of the NADPH requirements on the intracellular flux distribution. The two different approaches to the calculation of fluxes are compared and deviations in the results are discussed. Copyright 1998 John Wiley & Sons, Inc.     

Identification of Human Strains of Actinomyces viscosus

Catalase-positive actinomycetes which closely resemble the “hamster organism” described by Howell have been isolated from dental calculus and other human sources. These cultures could not be distinguished from the hamster strains on the basis of morphology, oxygen requirements, biochemical reactions, or cell wall composition. These human isolates have been classified with the hamster strains as Actinomyces viscosus. The strains from hamster and human sources fell into two serotypes. Serotype 1 contains the hamster strains plus one strain of unknown origin, whereas serotype 2 contains all of the human strains.     

Histopathological biomarkers and genotoxicity in gill and liver tissues of Nile tilapia Oreochromis niloticus from a polluted part of the Nile River,Egypt

Fish health is affected by water pollution. Oreochromis niloticus collected during summer 2014 from El-Serw, a polluted site on the Nile River, were compared with fish from a reference site, El-Zamalek. Histopathological changes were detected in gill and liver tissue samples using light and electron microscopy. In addition, the degree of DNA damage was measured using the comet assay. To indicate the severity of water pollution at the two sites, physico-chemical properties and heavy metal concentrations were investigated. Gill damage, including lamellar cell hyperplasia and aneurysm, was observed in the fish samples from the polluted site. The livers of fish from the polluted area showed necrosis and an increase in melanomacrophage centres. Histochemical results confirmed a marked rise of gill mucopolysaccharides and a reduction of carbohydrate stored in hepatocytes. Electron microscopy revealed clear alterations in gill and liver tissue of fish from the polluted site. The comet assay showed highly significant DNA damage in tilapia collected from the polluted site, compared to those from the reference site. Histopathological biomarkers and the comet assay may therefore be sensitive indicators of exposure to mixtures of aquatic pollutants in Nile tilapia.