Adaptive changes of rat liver cells induced by repeated intraperitoneal injections of d-galactosamine. III-Light- and electron-microscopic investigations of hepatocellular cytoplasmic changes.

In rats hepatocellular cytoplasmic changes after daily repeated D-galactosamine (GalN) intoxication--i.e. subacute GalN intoxication--were studied by light and electron microscopy. The number of GalN injections--and thus the days of survival--was between one and 30. The rats were killed six hours after the last GalN injection. Less degenerative changes were found after repeated GalN injections. An increased formation of atypical dense bodies (ADB), a temporary pronounced lipid accumulation and changes of the rough and smooth endoplasmic reticulum were prominent features of subacute GalN intoxication. The implications with respect to a modified GalN action in subacute GalN intoxication are discussed with special reference to biochemical data obtained in the same experimental model (Schuchhardt et al., 1977).     

The ectomycorrhizal basidiomycete Hebeloma circinans harbors a linear plasmid encoding a DNA- and RNA polymerase

Bulk DNA isolated from the ectomycorrhizal basidiomycete Hebeloma circinans was treated with proteinase K and submitted to agarose gel electrophoresis. In addition to high molecular weight genomic DNA, three minor bands were detected. The band with the highest electrophoretic mobility (2.2 kbp) corresponds to double-stranded RNA. The two other bands, termed pHC1 and pHC2, were shown to be dsDNA molecules of 10.3 and 9.1 kbp, respectively. Treatment of the pHC elements with 3'- and 5'-specific exonucleases revealed a linear structure and proved that the 5' ends are protected from digestion; for pHC2, linearity was confirmed by restriction mapping. A 3.2 kbp HindIII fragment of pHC2 was cloned and sequenced; it contains two open reading frames encoding putative viral B type DNA and RNA polymerases. Thus, the fungus harbors a typical linear plasmid, up to now, rarely described for basidiomycetes and hitherto unknown for mycorrhizal species.     

OntoGene in BioCreative II

Background:

Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the critical pieces of information that are needed to direct current and future research investment.

Results:

In this report we describe approaches taken within the scope of the second BioCreative competition in order to solve two aspects of this problem: detection of novel protein interactions reported in scientific articles, and detection of the experimental method that was used to confirm the interaction. Our approach to the former problem is based on a high-recall protein annotation step, followed by two strict disambiguation steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which deliver high-precision results while maintaining reasonable recall. The detection of the experimental methods is tackled by a pattern matching approach, which has delivered the best results in the official BioCreative evaluation.

Conclusion:

Although the results of BioCreative clearly show that no tool is sufficiently reliable for fully automated annotations, a few of the proposed approaches (including our own) already perform at a competitive level. This makes them interesting either as standalone tools for preliminary document inspection, or as modules within an environment aimed at supporting the process of curation of biomedical literature.