Bacteriophage MB78 DNA synthesis is specifically inhibited by the chelating agent ethylene diamine tetraacetic acid

The growth of bacteriophage MB78, a virulent phage of Salmonella typhimurium is extremely sensitive to the chelating agent EDTA. Other chelating agents like EGTA, a specific chelator for Ca²⁺ and orthophenanthroline which chelates Zn²⁺ and Fe²⁺ have no effect. EDTA stops phage MB78 DNA synthesis while synthesis of host DNA and other Salmonella phage DNA are not affected in presence of such low concentrations of EDTA. The present report indicates that some early phage function(s) and most probably the phage DNA synthesis are sensitive to EDTA which is probably due to chelation of Mg²⁺.     

The evolution of Queensland spiny mountain crayfish of the genus Euastacus. I. Testing vicariance and dispersal with interspecific mitochondrial DNA

The upland mesic rainforests of eastern Australia have been described as a "mesothermal archipelago" where a chain of cool mountain "islands" arise from a warm "sea" of tropical and subtropical lowlands. An endemic freshwater crayfish belonging to the genus Euastacus is found on each of these mountain "islands." The Euastacus are particularly suitable for the study of evolution because each mountain harbors a unique species, there are many taxa present providing replication within the group and, most importantly, their distribution is linear, extending along a south-north axis. This group could have evolved by "simultaneous vicariance" where there was one vicariant separation event of a widespread ancestor, or by "south to north stepping stone dispersal" where there were long distance dispersal events from neighboring mountain islands, starting in the south and proceeding north in a dispersal-colonization wave. We used pairwise genetic distances between nearest geographic neighbors as a novel way to test the two hypotheses. If diversification was due to "south to north stepping stone dispersal," then pairwise genetic distances between nearest geographic neighbors should decrease progressively the farther north the taxon pairs are found, reflecting the decreasing periods of isolation. In this case there should be a negative correlation between the south to north rank order of nearest neighbors and pairwise genetic distances. A Spearman's correlation on 16S mtDNA pairwise genetic distances and geographic rank order was not significant, indicating there was no support for the south to north stepping stone dispersal hypothesis. If simultaneous vicariance was responsible for diversification then all nearest geographic neighbor taxon pairs should have similar genetic distances and, therefore, the variance in nearest neighbor distances should be zero, or close to it. To test if the observed variance was tending towards zero we developed a randomization test where nearest neighbor taxon pairs were assigned random genetic distances and the variances calculated. The observed variance lay in the < 0.05 range of the simulated variances, providing support for the simultaneous vicariance hypothesis. The data also suggest there was simultaneous vicariance of at least two ancestral Queensland lineages. The timing of this vicariant event was probably in the Pliocene, which is consistent with the divergence times reported for other Australian mesic rainforest restricted taxa.     

Differentiation of Lactobacillus sanfranciscensis strains by randomly amplified polymorphic DNA and pulsed-field gel electrophoresis

Genetic diversity of Lactobacillus sanfranciscensis strains isolated from naturally fermented sourdoughs of different origin was evaluated by using randomly amplified polymorphic DNA (RAPD). Computer-assisted comparison of the RAPD patterns revealed a clear separation of L. sanfranciscensis from other obligately heterofermentative Lactobacillus species closely related or normally present in sourdough. Six clusters, five of them constituted by strains of the same origin, were recognized at a similarity level of 63%. Pulsed-field gel electrophoresis (PFGE) results on strains chosen as representative were generally in good agreement with the grouping obtained by RAPD. Both techniques showed a high degree of discriminatory power and indicated the existence of a remarkable genetic polymorphism within the species. Furthermore, the chromosome size of L. sanfranciscensis was estimated by PFGE to be about 1.4 Mb.     

A critique of the utility of the prediction of protein secondary structure

The Chou-Fasman predictive algorithm for determining the secondary structure of proteins from the primary sequence is reviewed. Many examples of its use are presented which illustrate its wide applicability, such as predicting (a) regions with the potential for conformational change, (b) sequences which are capable of assuming several conformations in different environments, (c) effects of single amino acid mutations, (d) amino acid replacements in synthesis of peptides to bring about a change in conformation, (e) guide to the synthesis of polypeptides with definitive secondary structure,e.g. signal sequences, (f) conformational homologues from varying sequences and (g) the amino acid requirements for amphiphilicα-helical peptides.     

ITS1 region of the rDNA of Pythium proliferatum, a new species: its taxonomy and its comparison with related species

A new species, Pythium proliferatum (F-382), was isolated from soil samples taken in Genlis in the burgundian region of France. The fungus is unique because of the character combinations of its large, spherical to elongated, proliferating sporangia, and its smooth walled oogonia supplied with different types of antheridia like hypogynous, monoclinous sessile, monoclinous stalked, diclinous and wrapping around the oogonia. Almost all types of antheridia that are found in the genus are present in this new species. Morphological features of this new species, together with the sequences of the ITS1 region of its nuclear ribosomal DNA and its comparison with related species are discussed in this article.     

Synthesis and crystal structures of water-soluble rhodium(III) complexes with 1,4,7-triazacyclononane and 2,2-bipyridine supporting ligands

New water-soluble rhodium(III) complexes with a tacn (1,4,7-triazacyclononane) and a bpy (2,2^′-bipyridine) supporting ligands were synthesized. The reaction of [Rh^III(tacn)Cl₃] (1) with equimolar amount of bpy and two equivalents of AgNO₃ in H₂O at reflux for 10 h gave a water-soluble chloro complex [Rh^III(tacn)(bpy)Cl](NO₃)₂ {2(NO₃)₂}. Complex 2(NO₃)₂ was treated with equimolar amount of AgNO₃ in H₂O at reflux for 10 h to give a water-soluble nitrato complex [Rh^III(tacn)(bpy)(NO₃)](NO₃)₂ {3(NO₃)₂}. Water-solubility of 3 with NO₃ ⁻ ligand (46.5 mg/mL) is high compared with that of 2 with Cl⁻ ligand (14.5 mg/mL) under the same conditions (at pH 7.0 at 25 °C). The structures of 2 and 3 were unequivocally determined by X-ray analysis. Their structures in H₂O were also examined by ¹H NMR, IR, and electrospray ionization mass spectrometry (ESI-MS).     

Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.     

Platelets do not express the oxidized or reduced forms of tissue factor

Background

Expression of tissue factor (TF) antigen and activity in platelets is controversial and dependent upon the laboratory and reagents used. Two forms of TF were described: an oxidized functional form and a reduced nonfunctional form that is converted to the active form through the formation of an allosteric disulfide. This study tests the hypothesis that the discrepancies regarding platelet TF expression are due to differential expression of the two forms.

Methods

Specific reagents that recognize both oxidized and reduced TF were used in flow cytometry of unactivated and activated platelets and western blotting of whole platelet lysates. TF-dependent activity measurements were used to confirm the results.

Results

Western blotting analyses of placental TF demonstrated that, in contrast to anti-TF#5, which is directed against the oxidized form of TF, a sheep anti-human TF polyclonal antibody recognizes both the reduced and oxidized forms. Flow cytometric analyses demonstrated that the sheep antibody did not react with the surface of unactivated platelets or platelets activated with thrombin receptor agonist peptide, PAR-1. This observation was confirmed using biotinylated active site-blocked factor (F)VIIa: no binding was observed. Likewise, neither form of TF was detected by western blotting of whole platelet lysates with sheep anti-hTF. Consistent with these observations, no FXa or FIXa generation by FVIIa was detected at the surface of these platelets. Similarly, no TF-related activity was observed in whole blood using thromboelastography.

Conclusion and significance

Platelets from healthy donors do not express either oxidized (functional) or reduced (nonfunctional) forms of TF.