ABSTRACT
The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
Subject(s)
Dictyostelium/genetics , Genome , Genomics , Social Behavior , ATP-Binding Cassette Transporters/genetics , Animals , Base Composition , Cell Adhesion/genetics , Cell Movement/genetics , Centromere/genetics , Conserved Sequence/genetics , DNA Transposable Elements/genetics , DNA, Ribosomal/genetics , Dictyostelium/cytology , Dictyostelium/enzymology , Dictyostelium/metabolism , Eukaryotic Cells/metabolism , Gene Duplication , Gene Transfer, Horizontal/genetics , Humans , Molecular Sequence Data , Phylogeny , Proteome , Protozoan Proteins/chemistry , Protozoan Proteins/genetics , RNA, Transfer/genetics , Repetitive Sequences, Nucleic Acid/genetics , Sequence Analysis, DNA , Signal Transduction/genetics , Telomere/geneticsABSTRACT
Proteins are composed of domains, which are conserved evolutionary units that often also correspond to functional units and can frequently be detected with reasonable reliability using computational methods. Most proteins consist of two or more domains, giving rise to a variety of combinations of domains. Another level of complexity arises because proteins themselves can form complexes with small molecules, nucleic acids and other proteins. The networks of both domain combinations and protein interactions can be conceptualised as graphs, and these graphs can be analysed conveniently by computational methods. In this review we summarise facts and hypotheses about the evolution of domains in multi-domain proteins and protein complexes, and the tools and data resources available to study them.
Subject(s)
Evolution, Molecular , Protein Structure, Tertiary/genetics , Proteins/genetics , Amino Acid Sequence , Animals , Computational Biology , Conserved Sequence/genetics , Conserved Sequence/physiology , Genetic Variation , Humans , Multiprotein Complexes/chemistry , Multiprotein Complexes/genetics , Protein Structure, Tertiary/physiology , Proteins/physiologyABSTRACT
This study describes the use of a shareware software package available from the National Institutes of Health for computing the fractal dimension. Specifically, when fractal analysis is used in its correct context it provides for a quantitative description of the space filling properties of two-dimensional objects. A rabbit model of post myocardial infarction is described where the cross-sectional infarct edge is reconstructed and its jaggedness determined by calculating its fractal dimension via the pixel dilation method. The fractal dimensions of the anterior and posterior lateral infarct edges were calculated to have a mean of 1.16 and 1.29, respectively. In conclusion, the fractal technique can be used to describe the complex jaggedness of the infarct edge. This case study also illustrates the fact that the complexity of an infarcted area is not uniform across the scar. For example, we found that the space filling properties of the anterior and posterior borders of a myocardial infarct can differ by more than 2-fold.
Subject(s)
Myocardial Infarction/pathology , Myocardium/pathology , Animals , Disease Models, Animal , Fractals , Image Processing, Computer-Assisted , Male , Rabbits , SoftwareABSTRACT
Previous studies have suggested that the jaggedness of the healed or healing infarct edge influences cardiac electrical stability. However, these findings have been based on histological observations rather than quantitative measurements. The aim of this study was to assess infarct jaggedness by calculating its fractal dimension and to examine how this influences cardiac electrical stability during late infarct healing in the rabbit. Using programmed electrical stimulation, it was found that the fractal dimension did not differ significantly in 19 rabbits that had inducible ventricular tachycardia and 16 that did not. We conclude from these studies in the mature rabbit that infarct edge jaggedness does not influence the ease with which ventricular tachycardia is induced during late myocardial infarct healing.
