A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.      

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Effect of growth factors and antigen on hybridoma cell culture dynamics

The cell growth and monoclonal antibody production kinetics of hybridoma cell cultures continuously exposed to growth factors and the cognate antigen were investigated. The growth factors were the epidermal growth factor, fibroblast growth factor, and interleukin-2, whereas the antigen was the trinitrophenyl group conjugated to a carrier protein. The cultures were carried out in a protein-free medium in batch operation. During the entire cultivation period there was continuously available free, antibody-unbound antigen to interact with the cells. The produced antibody was measured with an ELISA after it was released from the antigen-protein conjugate by competitive elution with non-protein-conjugated antigen. Cultures with growth factors and without antigen increased the total antibody produced by up to 30%, whereas cell growth remained unaffacted. Soluble antigen-protein conjugates had no effect on the hybridoma cultures. In contrast, immobilized antigen-protein on sepharose beads in cultures with growth factors induced significant changes. Total antibody produced was higher by up to 40%. More importantly, the specific antibody production shifted from a growth-phase-independent to a growth-phase-dependent profile, with approximately twice as much specific antibody production during the late growth-early stationary phase relative to constant specific antibody production in the antigen-free, factor-free culture. The culture changes induced by the presence of immobilized antigen and growth factors were reversed when the antigen and the growth factors were removed from the cells' environment. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 357-364, 1997.     

Widespread and ancient distribution of a noncanonical genetic code in diplomonads

Recently, a group of diplomonads has been found to use a genetic code in which TAA and TAG encode glutamine rather than termination. To survey the distribution of this characteristic in diplomonads, we sought to identify TAA and TAG codons at positions where glutamine is expected in genes for alpha-tubulin, elongation factor-1 alpha, and the gamma subunit of eukaryotic translation initiation factor-2. These sequences show that the variant genetic code is utilized by almost all diplomonads, with the genus Giardia alone using the universal genetic code. Comparative phylogenetic analysis reveals that the switch to this genetic code took place very early in the evolution of diplomonads and was likely a single event. Termination signals and downstream untranslated regions were also cloned from three Hexamita genes. In all three of these genes, the predicted TGA termination codon was found at the expected position. Interestingly, the untranslated regions of these genes are high in AT. This is incongruent with the coding regions, which are comparatively GC-rich.      

Immobilization of Acetobacter acoti on cellulose ion exchangers: adsorption isotherms

The adsorptive behavior of cells of Acetobacter aceti, ATCC 23746, on DEAE-, ECTEOLA-, TEAE-, and DEHPAE-cellulose ion exchangers in a modified Hoyer's medium at 30 degrees C was investigated. The maximum observed adsorption capacities varied from 46 to 64 mg dry wt/g resin. The Langmuir isotherm form was used to fit the data, since the cells formed a monolayer on the resin and exhibited saturation. The equilibrium constant in the Langmuir expression was qualitatively correlated with the surface charge density of the resin. The adsorption was also "normalized" by considering the ionic capacities of the resins. The exceptionally high normalized adsorption capacity of ECTEOLA-cellulose, 261 mg dry wt/meq, may be explained by an interaction between the cell wall and the polyglyceryl chains of the exchanging groups in addition to the electrostatic effects. The effect of pH on the bacterial adsorption capacity of ECTEOLA-, TEAE-, and phosphate-cellulose resins was studied and the pl of the bacteria was estimated to be 3.0.     

Trophic ecology and persistence of invasive silver carp Hypophthalmichthys molitrix in an oligotrophic South African impoundment

The alien invasive silver carp Hypophthalmichthys molitrix established a self-sustaining feral population in an oligotrophic impoundment, Flag Boshielo Dam, in South Africa. The ability of this population to persist in a dam with low algal biomass (median annual suspended chlorophyll a = 0.08 µg l^?1), and limited access to rivers considered large enough for successful spawning, has implications for their invasive potential in other systems. Stomach content and stable isotope analysis were used to assess the trophic ecology of H. molitrix, which was then compared with indigenous Mozambique tilapia Oreochromis mossambicus, on a seasonal basis during 2011. Hypophthalmichthys molitrix are generalist filter feeders, with a diet consisting primarily of sediment, vegetative detritus, dinoflagellates and diatoms. The dominance of sediments in their stomachs suggests occasional benthic scavenging. However, H. molitrix occupied a higher trophic level (TL = 2.8) than expected, suggesting that this population subsidised their diet with an unidentified dietary constituent, characterised by enriched nitrogen values. Although the stomach contents indicated dietary overlap between H. molitrix and O. mossambicus, stable isotopes revealed fine-scale resource partitioning, despite both species occupying the same trophic level. Nonetheless, the persistence of this feral H. molitrix population in an oligotrophic impoundment highlights their phenotypic plasticity.     

Extracting information from imaging cytometry: a review

The extraction of statistically meaningful quantitative information from microscopy images is increasingly important for modern biological research. Obtaining accurate, quantitative information from biological specimens, however, is a complex process that requires optimization of several parameters. One must consider the number of probes, fluorescent channels required, type of plate to be used, number of fields to be acquired and optimal resolution for image acquisition. The extraction of information from images is dependent on and can be aided greatly by careful consideration of the factors involved in the image acquisition process. I summarize here the general principles behind the imaging and software technology that is used to quantify images and highlight particular issues of concern for critically applying image quantitation techniques for research.