Bacterial populations in samples of bioleached copper ore as revealed by analysis of DNA obtained before and after cultivation.

The composition of bacterial populations in copper bioleaching systems was investigated by analysis of DNA obtained either directly from ores or leaching solutions or after laboratory cultures. This analysis consisted of the characterization of the spacer regions between the 16 and 23S genes in the bacterial rRNA genetic loci after PCR amplification. The sizes of the spacer regions, amplified from DNAs obtained from samples, were compared with the sizes of those obtained from cultures of the main bacterial species isolated from bioleaching systems. This allowed a preliminary assessment of the bacterial species present in the samples. Identification of the bacteria was achieved by partial sequencing of the 16S rRNA genes adjacent to the spacer regions. The spacer regions observed in DNA from columns leached at different iron concentrations indicated the presence of a mixture of different bacteria. The spacer region corresponding to Thiobacillus ferrooxidans was the main product observed at high ferrous iron concentration. At low ferrous iron concentration, spacer regions of different lengths, corresponding to Thiobacillus thiooxidans and "Leptospirillum ferrooxidans" were observed. However, T. ferrooxidans appeared to predominate after culture of these samples in medium containing ferrous iron as energy source. Although some of these strains contained singular spacer regions, they belonged within previously described groups of T. ferrooxidans according to the nucleotide sequence of the neighbor 16S rRNA. These results illustrate the bacterial diversity in bioleaching systems and the selective pressure generated by different growth conditions.     

Structural polypeptides of simian rotavirus SA11 and the effect of trypsin

Analysis of purified simian rotavirus has shown that it contains fewer structural polypeptide classes than previously reported. Two polypeptides (molecular weights, 62,000 and 28,000) commonly found in purified rotaviruses were, in fact, produced by cleavage of a larger structural polypeptide (molecular weight, about 88,000) by trypsin, which is usually employed to increase the yield of rotaviruses in tissue culture. Trypsin-uncleaved, double-shelled rotaviruses are probably composed of only five polypeptide classes; three in the inner layer, and two in the outer layer.     

The process of infection with bacteriophage φX174: XXXIX. The structure of a DNA form with restricted binding of intercalating dyes observed during synthesis of φX single-stranded DNA

A DNA form with restricted binding of intercalating dyes (propidium iodide or ethidium bromide) has been found in bacteriophage φX-infected cells during the period of single-stranded DNA synthesis. In the electron microscope, this DNA form is seen to be a double-stranded DNA ring with two single-stranded DNA tails protruding from the same portion of the ring; it is composed of a linear φX DNA strand, longer than one φX genome, and a single-stranded ring complementary to φX DNA. Base-pairing of these two tails in partially complementary regions restricts unwinding of the double-stranded DNA ring and consequently intercalation and binding of the dyes. It is postulated that these molecules originate from a previously reported precursor of φX DNA, namely a double-stranded ring with a single-stranded tail, by branch migration.     

Effect of Associated Bacteria on the Growth and Toxicity of Alexandrium catenella

Saprophytic bacteria in cultures of the marine dinoflagellate Alexandrium catenella were removed to assess their effect on growth and paralytic shellfish poisoning toxin production of this dinoflagellate. The actual axenic status was demonstrated by the lack of observable bacteria both immediately after treatment and following extended incubation in the absence of antibiotics. Bacteria were measured by counting CFU and also by epifluorescence microscopy and PCR amplification of bacterial 16S-23S spacer ribosomal DNA to detect noncultivable bacteria. Removal of bacteria did not have any effect on the growth of the dinoflagellate except for the inhibition of A. catenella disintegration after reaching the stationary phase. Toxicity was determined in dinoflagellate cell extracts by different methods: high-performance liquid chromatography (HPLC); an electrophysiological test called the Electrotest, which measures the inhibition of saxitoxin-sensitive Na⁺ channels expressed in a cell line; and a mouse bioassay, which measures the toxic effect on the whole mammal neuromuscular system. A lower toxicity of the dinoflagellates in axenic culture was observed by these three methods, though the difference was significant only by the mouse bioassay and HPLC methods. Altogether the results indicate that axenic cultures of A. catenella are able to produce toxin, though the total toxicity is probably diminished to about one-fifth of that in nonaxenic cultures.     

RIBOSOMAL RNA HETEROGENEITY AND IDENTIFICATION OF TOXIC DINOFLAGELLATE CULTURES BY HETERODUPLEX MOBILITY ASSAY

The heteroduplex mobility assay (HMA) reveals sequence dissimilarity between DNA by measuring the retarded migration of the hybrid or heteroduplex using polyacrylamide gel electrophoresis. Heterogeneity in some cultures of toxic dinoflagellates of the genus Alexandrium (Halim) Balech was observed during comparison of the amplified D1–D2 region of the large subunit rRNA gene (rDNA) using this method. HMA also allowed grouping of clones obtained from toxic bloom events in the Chilean, southernmost Pacific within the Asian Southern Pacific lineage of A. catenella (Whedon et Kofoid) Balech. The applied methodology provides a rapid and simple tool for use in assessing heterogeneity as well as for molecular grouping of strains among the genus Alexandrium.     

Detection by polmerase chain reaction-amplification and sequencing of an archaeon in a commercial-scale copper bioleaching plant

An archaeon was detected in the leaching solution from a commercial copper production plant and in copper sulfide ores leached with the solution. The leaching solution in this plant contains a high concentration of sulfate salts. Analysis of the microbial population by polymerase chain reaction-amplification of archaeal 16S rDNAs indicated the presence of a single sequence type. Comparison of the nucleotide sequence of the polymerase chain reaction product with available reference sequences suggested that this archaeon corresponds to a new species of a novel genus and family within the order Thermoplasmales. This archaeon grows in synthetic media but it has not been possible to obtain isolates free of chemolithotrophic bacteria.     

Determining the 3D structure of human ASC2 protein involved in apoptosis and inflammation

ASC2 structure has been well defined by 1141 NOE experimental restraints. The model consists of five alpha helices. alpha-Helices are connected by short random structure loops. The sole exception is the loop connecting helices 2 and 3, which has a 20-residue length. Folding generally agrees with the folding of recently published death domain structures in which alpha-helix structures have been reported. In spite of structural similarity, amino acid sequence homology with the most similar protein (ASC1) is just 64%. DD, DED, and CASP protein structures present six helices along their sequences; ASC2 presents 5 well-defined helices due to long distance restraints. However, a helical fragment was observed between amino acids 38 and 42 (representing helix 3) in the death domains when constructing the model.     

Polarized expression of CD74 by gastric epithelial cells.

CD74 is known as the major histocompatibility complex (MHC) class II-associated invariant chain (Ii) that regulates the cell biology and functions of MHC class II molecules. Class II MHC and Ii expression was believed to be restricted to classical antigen-presenting cells (APC); however, during inflammation, other cell types, including mucosal epithelial cells, have also been reported to express class II MHC molecules. Given the importance of Ii in the biology of class II MHC, we sought to examine the expression of Ii by gastric epithelial cells (GEC) to determine whether class II MHC molecules in these nonconventional APC cells were under the control of Ii and to further support the role that these cells may play in local immune and inflammatory responses during Helicobacter pylori infection. Thus we examined the expression of Ii on GEC from human biopsy samples and then confirmed this observation using independent methods on several GEC lines. The mRNA for Ii was detected by RT-PCR, and the various protein isoforms were also detected. Interestingly, these cells have a high level expression of surface Ii, which is polarized to the apical surface. These studies are the first to demonstrate the constitutive expression of Ii by human GEC.     

Evaluation of toxicity and degradation of a chlorophenol mixture by the laccase produced by Trametes pubescens

In this study, the biodegradation of a mixture of 2-chlorophenol (2-CP), 2,4-dichlorophenol (2,4-DCP), 2,4,6-trichlorophenol (2,4,6-TCP) and pentachlorophenol (PCP) using the laccase produced by the white-rot fungus Trametes pubescens CBS 696.94 was evaluated. Two laccase isoenzymes with molecular weights of about 60 and 120 kDa were identified in the enzymatic crude extract. The highest laccase activity with syringaldazine was observed with pH 6.0 and 60°C, while with 2,2-azino-bis(3-ethylbenzothiazoline-6) sulphonic acid the highest activity was observed between 50 and 60°C and 3.0-4.0 pH. A biodegradation of 100%, 99%, 82.1% and 41.1% for 2-CP, 2,4-DCP, 2,4,6-TCP and PCP, respectively, was observed after 4h of reaction. The reduction in chlorophenols concentration allowed 90% reduction in mixture toxicity. In summary, these results show the feasibility of a laccase enzymatic crude extract from T. pubescens for the reduction of concentration and toxicity of chlorophenols.