Reranking candidate gene models with cross-species comparison for improved gene prediction

Background  

Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features.     

A comparison of the chilling-stress response in two differentially tolerant cultivars of tomato (Lycopersicon esculentum).

The chilling responses of two differentially cold tolerant cultivars of tomato were monitored through in vivo labelling of polypeptides with [35S]methionine, both during a gradual temperature decrease (2 degrees C/day) and also during a rapid cold shock (4 degrees C). The polypeptides were separated by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and revealed by fluorography. Both cultivars showed changes in the polypeptide profiles resulting from either chilling treatment. During the gradual temperature decrease, there were few differences exhibited between the two cultivars. However, during cold shock both cultivars showed the altered synthesis of several unique polypeptides. Both cultivars showed the appearance of a 35-kDa polypeptide during the gradual temperature decrease and also during the cold shock. The appearance of three high relative mass polypeptides was found in both cultivars only during the gradual temperature decrease. Treatments with cycloheximide and chloramphenicol suggested that cold-shock polypeptides are both nuclear and organelle encoded. The cold-shock response in roots was different from the response in leaves and between cultivars. A comparison of the two cultivars showed a number of differences in polypeptide synthesis which may be related to increased cold tolerance.     

Reliability of Quality Assessments in Research Synthesis: Securing the Highest Quality Bioinformation for HIT

Current trends in bio-medicine include research synthesis and dissemination of bioinformation by means of health (bio) information technology (H[b] IT). Research must secure the validity and reliability of assessment tools to quantify research quality in the pursuit of the best available evidence. Our concerted work in this domain led to the revision of three instruments for that purpose, including the stringent characterization of inter-rater reliability and coefficient of agreement. It is timely and critical to advance the methodological development of the science of research synthesis by strengthening the reliability of existing measure of research quality in order to ensure H[b] IT efficacy and effectiveness.     

Hemolytic uremic syndrome in renal allografted patients treated with cyclosporin

The classical triad of hemolytic uremic syndrome (microangiopathic hemolytic anemia, severe thrombopenia, and renal failure) developed de novo in three of our renal transplanted patients under cyclosporin A treatment. The predominant morphologic findings in the grafts consisted of glomerular and arteriolar thrombosis as well as arteriolonecrosis, all features of the syndrome. In one instance, ischemic bowel disease supervened after graft removal and was associated with persistent low grade microangiopathic process. De novo hemolytic uremic syndrome has been reported in patients treated with cyclosporin A following bone marrow or liver transplantation as well as in a few renal graft recipients. This peculiar form of cyclosporin A nephrotoxicity should not be confused with acute rejection of the renal transplant.     

Fitting progress curves in assays of slow-binding enzyme inhibitors.

Practical aspects of fitting progress curves deriving from assays of slow-binding enzyme inhibitors in order to extract characteristic parameters is briefly discussed. An approach little-used, but which may provide more accurate estimates, is the simultaneous analysis of two assays differing from one another in the order of addition of reactants.