Protistan microbial observatory in the Cariaco Basin,Caribbean. I. Pyrosequencing vs Sanger insights into species richness

Microbial diversity and distribution are topics of intensive research. In two companion papers in this issue, we describe the results of the Cariaco Microbial Observatory (Caribbean Sea, Venezuela). The Basin contains the largest body of marine anoxic water, and presents an opportunity to study protistan communities across biogeochemical gradients. In the first paper, we survey 18S ribosomal RNA (rRNA) gene sequence diversity using both Sanger- and pyrosequencing-based approaches, employing multiple PCR primers, and state-of-the-art statistical analyses to estimate microbial richness missed by the survey. Sampling the Basin at three stations, in two seasons, and at four depths with distinct biogeochemical regimes, we obtained the largest, and arguably the least biased collection of over 6000 nearly full-length protistan rRNA gene sequences from a given oceanographic regime to date, and over 80 000 pyrosequencing tags. These represent all major and many minor protistan taxa, at frequencies globally similar between the two sequence collections. This large data set provided, via the recently developed parametric modeling, the first statistically sound prediction of the total size of protistan richness in a large and varied environment, such as the Cariaco Basin: over 36 000 species, defined as almost full-length 18S rRNA gene sequence clusters sharing over 99% sequence homology. This richness is a small fraction of the grand total of known protists (over 100 000–500 000 species), suggesting a degree of protistan endemism.     

The use of bromodeoxyuridine labeling in the human lymphocyte HGPRT somatic mutation assay

The autoradiographic assay developed by Strauss and Albertini (1979) to quantitate human in vivo somatic mutation at the hypoxanthine guanine phosphoribosyl-transferase locus uses tritiated thymidine to identify mutant cells by their ability to pass through 'S' phase in the presence of 6-thioguanine. An alternative method, based on the incorporation of bromodeoxyuridine (BrdUrd) into the DNA of proliferative cells, followed by differential staining with the fluorescence-plus-Giemsa method, was used to identify 3 classes of lymphocyte nuclei: (a) small darkly stained nuclei, (b) large, reddish-colored nuclei with an apparent nucleolus, and (c) large, bluish-colored nuclei. By double labeling with BrdUrd and tritiated thymidine, it was determined that only the nuclei of the third class had incorporated BrdUrd. These results demonstrate that the technique used for sister-chromatid differentiation can be used to detect putative HGPRT mutants and to determine variant frequencies at the HGPRT locus.     

Studies on evolutionary and selective properties of hypercycles using a Monte Carlo method

Summary The most relevant properties of hypercycles were previously studied mainly from a theoretical point of view. We have developed a Monte Carlo method simulating hypercyclic organization to obtain information about the dynamics of this prebiotic organization. Nucleation, growth, and selective properties have been tested and the results obtained are in good agreement with those of the theoretical predictions. The influence of hypercyclic organization of the error threshold has also been studied. As a consequence of the emergence of a hypercycle, the value of this threshold decreases. The amount of this decrease depends on the population size. Moreover, for some interval of quality factor values, either the hypercycle organization or an error catastrophe can be produced, depending on the initial conditions. The influence of these phenomena on both the dynamic behavior and evolutionary advantages of the hypercycle, as well as their decisive roles on genome size, are discussed.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Effects of anisosmotic buffers on K+ transport in isolated chicken enterocytes

Cells isolated by hyaluronidase incubation from chicken small intestine were used to study the effects of anisosmotic buffers on K+ transport. Hypo-osmolarity (200 mosmol.l-1) reduced both the ouabain-sensitive and the ouabain-resistant, but bumetanide-sensitive, net K+ influx and increased the K+ efflux. The hypo-osmolarity induced K+ efflux was prevented by quinine and unaffected by bumetanide. These results suggest that Ca2+-activated K+ channels may be involved in regulatory volume decrease in chicken enterocytes. Hyperosmotic conditions (400 mosmol.l-1) increased the portion of net K+ influx mediated by the Na+/K+-ATPase and that mediated by the bumetanide-sensitive K+ transport system, and decreased the K+ efflux.     

A re-examination of the Na+-independent binding of [3H]β-alanine to rat brain stem-spinal cord

The Na⁺-independent binding of [³H]-alanine to rat brain stem plus spinal cord was reinvestigated, in order to study in more detail the characteristics of previously described -alanine binding processes. Binding was absent when amino acid-free postnuclear supernatants or crude synaptic membranes were used. Experiments performed with several other Na⁺-free preparations showed a sole binding component, irrespective of the preparation used. Biochemical characterization of this Na⁺-independent binding, using frozen/thawed/washed synaptosomal-mitochodrial fractions, showed that binding reached a plateau between 7 min and 13 min, increasing thereafter. Binding was linear with fraction protein over a range of 200–415 g/ml incubation medium. Binding was completely inhibited by glycine, alanine, -aminobutyric acid, -aminoisobutyric acid, hypotaurine and strychnine, and to a lesser extent by 2,2-dimethyl--alanine, brucine and gelsemine. It was insensitive to taurine, -aminobutyric acid (GABA), 2-guanidinoethanesulfonic acid (GES), carnosine, and bicuculline methiodide. Binding was reversible, saturable (K _D 20 M), and heat sensitive.     

Detection and quantification of patulin and griseofulvin by high pressure liquid chromatography in different strains of Penicillium griseofulvum Dierckx

Patulin and griseofulvin production by twelve strains ofPenicillium griseofulvum Dierckx, eleven of which were isolated from pistachio (Pistacia vera) nuts and the other was supplied by the Spanish Collection of Type Culture, was investigated. Six strains of the eleven isolated had ability to produce patulin and griseofulvin in Yes medium. All the strains studied had no ability to produce patulin in Wickerham medium. Griseofulvin production was significant in both media but higher in Wickerham. These metabolites were separated and determined in the chloroform extracts of cultures by high performance liquid chromatography with ultraviolet detection. The best conditions were: acetonitrile — water (45∶55) as mobile phase, a flow rate of 2.0 mL/min and a μ Bondapack C₁₈ column.     

HLA gene and haplotype frequencies in galicia (NW Spain)

The genetic structure of six populations of Iran (Turks, Kurds, Lurs, Zabolis, Baluchis and Zoroastrians) was examined using data on blood groups, serum proteins and cell enzymes. Our results show conclusively that there are genetic differences among the six populations and the analysis of superimposed R and S matrices defined by Harpending & Jenkins (1973) show that the dispersion of some of the alleles correspond to the dispersion of the populations. The F_ST estimates are not large enough to favour selection on any of the loci studied. The F_IT and F_IS estimates are positive and moderately high suggesting that the genetic differentiation to some extent is influenced by inbreeding.