Benthic feeding by krill, Euphausia superba Dana, in coastal waters off West Antarctica and in Admiralty Bay, South Shetland Islands

Diatoms in the food of krill caught in the summer in coastal waters close to the South Shetland Islands and in the summer and three winters in Admiralty Bay, King George Island were investigated. The diatoms were used as indicators of sources of krill food. Principal component analysis divided the diatom taxa into two groups, one being pelagic diatoms and from the food of krill in coastal waters, and the other being benthic diatoms and taxa from the food of krill in Admiralty Bay. All pelagic taxa of diatoms were consumed by krill. In the summer in coastal waters, benthic diatoms in krill food originated from the sublittoral. In the summer in Admiralty Bay, besides phytoplankton, diatoms were noted from the sublittoral and littoral in the food of krill. However, in the winter mostly sublittoral and epiphytic diatoms were present in krill food. Accepted: 20 March 2000     

Mg2+ effects on a circle opening reaction of the self-splicing intervening sequence from Tetrahymena thermophila

The Mg2+ contribution to the reaction of circular intervening sequence (CIVS) from rRNA precursor of Tetrahymena thermophila with a dinucleotide CU has been investigated. The results indicated that the circle opening of CIVS may involve binding of a weakly held Mg2+ ion.     

Modeling and simulation of the main metabolism in <Emphasis Type="Italic">Escherichia coli</Emphasis> and its several single-gene knockout mutants with experimental verification

Background  

It is quite important to simulate the metabolic changes of a cell in response to the change in culture environment and/or specific gene knockouts particularly for the purpose of application in industry. If this could be done, the cell design can be made without conducting exhaustive experiments, and one can screen out the promising candidates, proceeded by experimental verification of a select few of particular interest. Although several models have so far been proposed, most of them focus on the specific metabolic pathways. It is preferred to model the whole of the main metabolic pathways in Escherichia coli, allowing for the estimation of energy generation and cell synthesis, based on intracellular fluxes and that may be used to characterize phenotypic growth.     

MetaMQAP: A meta-server for the quality assessment of protein models

Background  

Computational models of protein structure are usually inaccurate and exhibit significant deviations from the true structure. The utility of models depends on the degree of these deviations. A number of predictive methods have been developed to discriminate between the globally incorrect and approximately correct models. However, only a few methods predict correctness of different parts of computational models. Several Model Quality Assessment Programs (MQAPs) have been developed to detect local inaccuracies in unrefined crystallographic models, but it is not known if they are useful for computational models, which usually exhibit different and much more severe errors.     

Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides

Thermodynamic parameters for bulge loops of one to three nucleotides in oligoribonucleotide duplexes have been measured by optical melting. The results indicate bulges Bn of An and Un have similar stabilities in the duplexes, GCGBmGCG + CGCCGC. The stability increment for a bulge depends on more than its adjacent base pairs. For example, the stability increment for a bulge is affected more than 1 kcal/mol by changing two nonadjacent base pairs or by adding terminal unpaired nucleotides (dangling ends) three base pairs away. Thus a nearest-neighbor approximation for helixes with bulges is oversimplified. Many of the non-self-complementary strands used in this study were observed to form homoduplexes. Such duplexes with GA mismatches were particularly stable.     

Winter food caches of beavers<Emphasis Type="Italic">Castor fiber</Emphasis> in NE Poland

Winter food caches of beaversCastor fiber Linnaeus, 1758 were examined in 16 locations within the Suwałki region (north-eastern Poland). Four caches were selected to represent each of four habitat types: river, lake, farmland, and oligotrophic small reservoir called ‘suchar’. Altogether, 92 509 twigs and branches of 15 woody species were identified and measured. Individual caches, with one exception, included branches of only 4 or 5 species. WillowsSalix sp., birchesBetula sp., alderAlnus glutinosa, trembling aspenPopulus tremula, and mountain ashSorbus aucuparia occurred in caches from all four habitats studied. Willows alone constituted 62.5% of the total number of branches cached. Willows, together with birch, hazelCorylus avellana, alder, and trembling aspen, amounted to 97% of all branches in caches. The remaining 10 species provided only 3% of the branches cached. Most branches were 0.5–1 m long and <3 cm thick at their base. Contents of food caches provided a good indication of winter diet and possibly food preference of beavers.     

Involvement of the Pseudomonas aeruginosa MexAB–OprM efflux pump in the secretion of the metallophore pseudopaline

To overcome the metal restriction imposed by the host’s nutritional immunity, pathogenic bacteria use high metal affinity molecules called metallophores. Metallophore‐mediated metal uptake pathways necessitate complex cycles of synthesis, secretion, and recovery of the metallophore across the bacterial envelope. We recently discovered staphylopine and pseudopaline, two members of a new family of broad‐spectrum metallophores important for bacterial survival during infections. Here, we are expending the molecular understanding of the pseudopaline transport cycle across the diderm envelope of the Gram‐negative bacterium Pseudomonas aeruginosa. We first explored pseudopaline secretion by performing in vivo quantifications in various genetic backgrounds and revealed the specific involvement of the MexAB–OprM efflux pump in pseudopaline transport across the outer membrane. We then addressed the recovery part of the cycle by investigating the fate of the recaptured metal‐loaded pseudopaline. To do so, we combined in vitro reconstitution experiments and in vivo phenotyping in absence of pseudopaline transporters to reveal the existence of a pseudopaline modification mechanism, possibly involved in the metal release following pseudopaline recovery. Overall, our data allowed us to provide an improved molecular model of secretion, recovery, and fate of this important metallophore by P. aeruginosa.     

DNA-protein cross-linking in L1210 cells sensitive and resistant to cis-diamminedichloroplatinum (II)

The role of restricted cellular accumulation of cis-diamminedichloroplatinum(II) (cis-DDP) and altered repair of DNA-Pt-protein cross-links in the mechanism of L1210 murine leukemia cell resistance was examined. An immunochemical method was used to analyze the formation and removal of DNA-Pt-protein complexes in L1210 cells sensitive and resistant to cis-DDP. The accumulation of Pt into the cells and the binding of Pt to the DNA was measured by atomic absorption spectroscopy. The results demonstrated that both decreased accumulation of the drug and the rate of DNA-Pt protein cross-link removal may be important factors in L1210 cell resistance to cis-DDP.Abbreviations AAS atomic absorption spectroscopy - cis-DDP cis-diamminedichloroplatinum(II)