The importance of alternative splicing in many genomes has raised interesting questions about its role in evolution. We analyzed 13 384 full-length transcript isoforms from human and 2227 isoforms from mouse to identify sequences containing premature termination codons (PTCs) that are likely targets of mRNA nonsense-mediated decay. We found that alternatively spliced isoforms have a much higher...

Bacteria regulate chromosome replication and segregation tightly with cell division to ensure faithful segregation of DNA to daughter generations. The underlying mechanisms have been addressed in several model species. It became apparent that bacteria have evolved quite different strategies to regulate DNA segregation and chromosomal organization. We have investigated here how the actinobacteri...

PURPOSE Colorectal carcinoma (CRC) can be divided into two nonoverlapping groups: those that are chromosomally unstable but microsatellite stable (MSS CIN+) and those that are chromosomally stable but microsatellite unstable (MSI CIN-). However, a third group with neither chromosome nor microsatellite instability (MSS CIN-) makes a substantial contribution to the total CRC burden. The clinicopa...

This paper develops mathematical models describing the evolutionary dynamics of both asexually and sexually reproducing populations of diploid unicellular organisms. The asexual and sexual life cycles are based on the asexual and sexual life cycles in Saccharomyces cerevisiae, or Baker’s yeast, which normally reproduces by asexual budding, but switches to sexual reproduction when stressed. The ...

We have studied human spermatozoa from 24 normal, healthy unexposed men, 18 of whom were semen donors at the Sperm Bank in Turku, using multicolor fluorescence in situ hybridization with two chromosome-specific probes. The possible age-related increase in aneuploidy frequencies was assessed. Ten thousand spermatozoa were scored per individual for the presence of hyperploid, i.e., disomic and di...

Polyploidization has crucial impacts on the evolution of different eukaryotic lineages including fungi, plants and animals. Recent genome data suggest that, for many polyploidization events, all duplicated chromosomes are maintained and genome reorganizations occur much later during evolution. However, newly-formed polyploid genomes are intrinsically unstable and often quickly degenerate into a...

We studied the relationships between genetic and epigenetic alterations in gastrointestinal cancer by integrating DNA copy number changes determined by arbitrarily primed PCR (AP-PCR) with DNA methylation variations estimated by methylation-sensitive amplified fragment length polymorphism (MS-AFLP). We analyzed about 100 different chromosomal regions by AP-PCR and over 150 random CpG loci by MS...

Arabidopsis thaliana is widely accepted as a model species in plant biology. Its genome, due to its small size and diploidy, was the first to be sequenced among plants, making this species also a reference for plant comparative genomics. Nevertheless, the evolutionary mechanisms that shaped the Arabidopsis genome are still controversial. Indeed, duplications, translocations, inversions, and gen...

When working in changing environments, it is important for a solution approach to adapt to the change and follow the new optima. For genetic algorithms, using diploid representations is one of the methods for addressing performance and diversity issues in such environments. When using a diploid representation for individuals, the choice of a good genotype to phenotype mapping mechanism is a ver...

Flow cytometric analyses of cellular DNA, RNA, and double-stranded RNA content were performed on lymph nodes and extranodal tissue from 177 patients with non-Hodgkin's lymphoma. With increasing histologic grade, a higher incidence of aneuploidy, higher proliferative activity, and higher total and double-stranded RNA content were found. Despite considerable cytometric heterogeneity within histol...